#-----------------------------------------------------------+ # | # WHEAT.TIERS - APOLLO TIERS FILE | # WORKING DRAFT | # | #-----------------------------------------------------------+ # | # AUTHOR : JAMES C. ESTILL | # STARTED: 02/08/2007 | # UPDATED: 04/24/2007 | # DESCRIPTION: | # | # This tiers file has a focus on gene model annotation. | # Other seq feature result information (RNAS, TEs, etc. | # could potentially use a separate tiers file. Using | # separate tiers files for different aspects of annotation | # will allow a wider color space for each of the | # individual annotation methods. | # | #-----------------------------------------------------------+ #-----------------------------------------------------------+ # TO DO | #-----------------------------------------------------------+ # [ ] Edit the default names to work with the format that # we will be using for wheat annotation. # [ ] Add the rest of the potential PUTs databases #-----------------------------------------------------------+ # TIER FIELDS | #-----------------------------------------------------------+ # # label : false (Group tier label) # visible : true # expanded : false # sorted : false # maxrows : maximum number of rows to show for this tier # --default 0 means all # labeled : false # curated : false # [Whether to display in blue annotation zone] # warnonedit : false # [Can also be used as a Type parameter to tag # individual types] # number_of_levels : 3 # [The default is 1, for one-level annotation # types; use 3 for gene-like annotations # (gene/transcript/exon)] # # The order in which tiers are listed in this file determines # their vertical display order (the first tier is displayed # closest to the central axis). # #-----------------------------------------------------------+ #-----------------------------------------------------------+ # TYPE FIELDS | #-----------------------------------------------------------+ # tiername : the tier this type appears in # typename : label for this type # resulttype : data type(s) to be included this type # You may have mutliple resultypes listed # to pull in the same result from multiple # sources # color : can be a standard color name (e.g. red) or an # R,G,B triplet (default gray) # utr_color : color used for utr regions. Only works with # DrawableGeneFeatureSet. (default black) # usescore : default true # use score to set the height of this glyph # minscore : 0 # minimum score for scaling height # maxscore : 100 # maximum score for scaling height # glyph : what glyph to use (mandatory). # Current choices include: # DrawableGeneFeatureSet (exons & peaked introns), # DrawableResultFeatureSet (exons & straight lines), # DoubleHeadedArrow, # Triangle, # Zigzag, # ThinRectangle (a rectangular outline). # column : names of column(s) in detail table. Choices include # GENOMIC_RANGE, # GENOMIC_LENGTH, # MATCH_RANGE, # MATCH_LENGTH, # SCORE, # NAME, # READS. # You can also specify column names not in all caps # that correspond to properties of the features present # in the data (e.g.query_frame). # sortbycolumn : row order in table determined by this column # reversesort : Sort table rows in reverse order? (default false) # groupby : GENE method to use for grouping features # (GENE, SINGLE, HOMOLOGY) # weburl : optional, URL for pulling up web # pages about this type of result # freshdate : date after which sequences of this type are # considered new (the dates are found in the # sequence descriptions) # idformat : format of IDs for this kind of annotation # (regexp, e.g. CG\d+) # annot_type : when this result is promoted to an annotation, # annot_type says which type of annotation it # should become. # warnonedit : false [Overrides value of warnonedit setting, if any, # for the parent tier] # # The fields for a Type or Tier record can appear in any order, one per # line. Be sure that none of the lines get broken up by inserted newlines. #-----------------------------------------------------------+ #-----------------------------------------------------------+ # ANNOTATION | #-----------------------------------------------------------+ #-----------------------------------------------------------+ # These are the main annotation features that appear on the # annotation panes of Apollo. [Tier] tiername : Annotation expanded : true labeled : true curated : true warnonedit : false #-----------------------------+ # GENE | #-----------------------------+ # Using DPgn for Dawg Paws Gene for now [Type] label : gene tiername : Annotation datatype : gene datatype : transcript datatype : exon glyph : DrawableGeneFeatureSet color : 51,102,255 idformat : DPgn\d{7} utr_color : 176,224,230 name_method : FlyNameAdapter overlap_method : ORF_Overlap column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE number_of_levels : 3 #-----------------------------+ # GAP | #-----------------------------+ # ADDED BY JAMIE 02/20/2007 # This will be used to show gaps in the [Type] label : gap tiername : Annotation datatype : gene datatype : transcript datatype : exon glyph : Zigzag color : 255,0,0 //utr_color : 176,224,230 //overlap_method : ORF_Overlap column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE name_method : FlyNameAdapter idformat : DPgap\d{7} ##-----------------------------+ ## Transfer RNA | ##-----------------------------+ #[Type] #label : tRNA #tiername : Annotation #datatype : tRNA #glyph : DrawableResultFeatureSet #color : 0,204,0 #idformat : FBgn\d{7} #name_method : FlyNameAdapter #overlap_method : ORF_Overlap #column : GENOMIC_RANGE #column : ID #sortbycolumn : GENOMIC_RANGE # # ##-----------------------------+ ## Small Nuclear RNA | ##-----------------------------+ #[Type] #label : snRNA #tiername : Annotation #datatype : snRNA #glyph : DrawableResultFeatureSet #color : 0,204,0 #idformat : FBgn\d{7} #name_method : FlyNameAdapter #overlap_method : ORF_Overlap #column : GENOMIC_RANGE #column : ID #sortbycolumn : GENOMIC_RANGE # ##-----------------------------+ ## Small Nucleolar RNA | ##-----------------------------+ #[Type] #label : snoRNA #tiername : Annotation #datatype : snoRNA #glyph : DrawableResultFeatureSet #color : 0,204,0 #idformat : FBgn\d{7} #name_method : FlyNameAdapter #overlap_method : ORF_Overlap #column : GENOMIC_RANGE #column : ID #sortbycolumn : GENOMIC_RANGE # ##-----------------------------+ ## Non-Coding RNA | ##-----------------------------+ #[Type] #label : ncRNA #tiername : Annotation #datatype : misc. non-coding RNA #datatype : ncRNA #glyph : DrawableResultFeatureSet #color : 0,204,0 #idformat : FBgn\d{7} #name_method : FlyNameAdapter #overlap_method : ORF_Overlap #column : GENOMIC_RANGE #column : ID #sortbycolumn : GENOMIC_RANGE # ##-----------------------------+ ## Ribosomal RNA | ##-----------------------------+ #[Type] #label : rRNA #tiername : Annotation #datatype : rRNA #glyph : DrawableResultFeatureSet #color : 0,204,0 #idformat : FBgn\d{7} #name_method : FlyNameAdapter #overlap_method : ORF_Overlap #column : GENOMIC_RANGE #column : ID #sortbycolumn : GENOMIC_RANGE # ##-----------------------------+ ## MicroRNA | ##-----------------------------+ #[Type] #label : miRNA #tiername : Annotation #datatype : microRNA #datatype : miRNA #glyph : DrawableResultFeatureSet #color : 0,204,0 #idformat : FBgn\d{7} #name_method : FlyNameAdapter #overlap_method : ORF_Overlap #column : GENOMIC_RANGE #column : ID #sortbycolumn : GENOMIC_RANGE #-----------------------------+ # Pseudogene | #-----------------------------+ [Type] label : pseudogene tiername : Annotation datatype : pseudogene glyph : DrawableResultFeatureSet color : 153,153,255 idformat : DPgn\d{7} name_method : FlyNameAdapter overlap_method : ORF_Overlap column : GENOMIC_RANGE column : ID number_of_levels : 3 //-----------------------------------------------------------+ // Dispersed Repeats | //-----------------------------------------------------------+ // At the minimum I want to make this a tier separate from // the regular Annotation Field. This will allow me to // collapse the DRDs from the TRDs // However trying to get this to collapse does not // really seem to be working. I will leave this in the // annotation tier for now while I work with the results // tiers. // --JCE 02/13/2007 //[Tier] //tiername : Dispersed Repeats //expanded : true //labeled : true //curated : true //warnonedit : false [Type] label : transposable_element tiername : Annotation //tiername : Dispersed Repeats datatype : transposable_element // Jamie added the following two datatype : LTR datatype : repeat_region glyph : DoubleHeadedArrow color : 255,0,203 idformat : DPte\d{7} name_method : FlyNameAdapter overlap_method : NoOverlap column : ID column : GENOMIC_RANGE sortbycolumn : GENOMIC_RANGE groupby : HOMOLOGY warnonedit : true number_of_levels : 1 #-----------------------------------------------------------+ #-----------------------------------------------------------+ # OTHER ANNOTATED FEATURES | #-----------------------------------------------------------+ #-----------------------------------------------------------+ [Tier] # JCE turned on labeling 02/28/2007 tiername : Other annotated features # expand while testing expanded : true labeled : true curated : true warnonedit : true //[Type] //label : P insertion_site //tiername : Other annotated features //datatype : p_insertion //datatype : P insertion_site //datatype : transposable_element_insertion_site //datatype : insertion_site //glyph : Triangle //color : 255,0,203 //idformat : FBti\d{7} //name_method : FlyNameAdapter //overlap_method : NoOverlap //# column : SCORE //column : ID //column : GENOMIC_RANGE //column : GENOMIC_LENGTH //sortbycolumn : GENOMIC_RANGE //number_of_levels : 1 [Type] label : remark tiername : Other annotated features datatype : miscellaneous curator's observation datatype : remark glyph : Zigzag color : 255,255,204 idformat : CR\d+ name_method : FlyNameAdapter overlap_method : NoOverlap column : GENOMIC_RANGE column : ID number_of_levels : 1 //# ARGS types //[Type] //label : rescue fragment //tiername : Other annotated features //datatype : rescue_fragment //glyph : ThinRectangle //color : 153,51,255 //name_method : FlyNameAdapter //overlap_method : NoOverlap //column : ID //column : GENOMIC_RANGE //column : GENOMIC_LENGTH //sortbycolumn : GENOMIC_RANGE //number_of_levels : 1 //[Type] //label : point mutation //tiername : Other annotated features //datatype : point_mutation //glyph : Triangle //color : 0,102,204 //name_method : FlyNameAdapter //overlap_method : NoOverlap //column : ID //column : GENOMIC_RANGE //sortbycolumn : GENOMIC_RANGE //number_of_levels : 1 //[Type] //label : protein binding site //tiername : Other annotated features //datatype : protein_binding_site //glyph : DrawableResultFeatureSet //color : 255,204,0 //name_method : FlyNameAdapter //overlap_method : NoOverlap //column : ID //column : GENOMIC_RANGE //column : GENOMIC_LENGTH //sortbycolumn : GENOMIC_RANGE //number_of_levels : 1 //[Type] //label : sequence variant //tiername : Other annotated features //datatype : sequence_variant //glyph : ThinRectangle //color : 0,153,255 //name_method : FlyNameAdapter //overlap_method : NoOverlap //column : ID //column : GENOMIC_RANGE //column : GENOMIC_LENGTH //sortbycolumn : GENOMIC_RANGE //number_of_levels : 1 //[Type] //label : aberration junction //tiername : Other annotated features //datatype : aberration_junction //glyph : Zigzag //color : 153,0,51 //name_method : FlyNameAdapter //overlap_method : NoOverlap //column : ID //column : GENOMIC_RANGE //column : GENOMIC_LENGTH //sortbycolumn : GENOMIC_RANGE //number_of_levels : 1 //[Type] //label : regulatory region //tiername : Other annotated features //datatype : regulatory_region //glyph : DrawableResultFeatureSet //color : 102,255,255 //name_method : FlyNameAdapter //overlap_method : NoOverlap //column : ID //column : GENOMIC_RANGE //column : GENOMIC_LENGTH //sortbycolumn : GENOMIC_RANGE //number_of_levels : 1 [Type] label : region tiername : Other annotated features datatype : region glyph : DrawableResultFeatureSet color : 102,255,255 name_method : FlyNameAdapter overlap_method : NoOverlap column : ID column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE number_of_levels : 1 [Type] label : oligonucleotide tiername : Other annotated features datatype : oligonucleotide glyph : DrawableResultFeatureSet color : 204,102,0 name_method : FlyNameAdapter overlap_method : NoOverlap column : ID column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE number_of_levels : 1 [Type] label : DNA motif tiername : Other annotated features datatype : DNA_motif glyph : ThinRectangle color : 102,102,102 name_method : FlyNameAdapter overlap_method : NoOverlap column : ID column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE number_of_levels : 1 //[Type] //label : enhancer //tiername : Other annotated features //datatype : enhancer //glyph : DrawableResultFeatureSet //color : 255,153,255 //name_method : FlyNameAdapter //overlap_method : NoOverlap //column : ID //column : GENOMIC_RANGE //column : GENOMIC_LENGTH //sortbycolumn : GENOMIC_RANGE //number_of_levels : 1 //[Type] //label : mature peptide //tiername : Other annotated features //datatype : mature_peptide //glyph : DrawableResultFeatureSet //color : 102,102,255 //column : ID //name_method : FlyNameAdapter //overlap_method : NoOverlap //column : GENOMIC_RANGE //number_of_levels : 1 //[Type] //label : signal peptide //tiername : Other annotated features //datatype : signal_peptide //glyph : DrawableResultFeatureSet //color : 153,153,255 //name_method : FlyNameAdapter //overlap_method : NoOverlap //column : ID //column : GENOMIC_RANGE //number_of_levels : 1 #-----------------------------------------------------------+ #-----------------------------------------------------------+ # COMPUTATIONAL RESULTS TYPES | #-----------------------------------------------------------+ #-----------------------------------------------------------+ # THE FOLLOWING TIERS ARE COMPUTATIONAL RESULTS THAT CAN # BE ADDED TO THE ANNOTATION TIERS ABOVE #-----------------------------------------------------------+ # NEW ANALYSIS RESULTS | #-----------------------------------------------------------+ # This is the default type used by Apollo when adding # data from the computational analysis panel [Tier] tiername : New analysis results expanded : true labeled : true [Type] label : New analysis results tiername : New analysis results glyph : DrawableResultFeatureSet color : 255,255,0 usescore : true column : SCORE column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # E. coli BLASTN | #-----------------------------------------------------------+ # ADDED 03/01/2007 # This will highlight PROBLEMS in the assembly # Red empty boxes these will be the nearest to the central # axis to highlight some problem regions # [Tier] tiername : Contamination expanded : true labeled : true #-----------------------------+ # E. coli BLASTN | #-----------------------------+ # 03/01/2007 # ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/ # E coli genomes are # 03/03/2007 # Changed glyph from ThinRectangle [Type] typename : E. coli BLASTN tiername : Contamination datatype : blastn:contam_Ecoli glyph : ThinRectangle //glyph : DrawableResultFeatureSet color : 255,0,0 usescore : true column : SCORE column : expect column : identity column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------+ # NCBI UniVec BLASTN | #-----------------------------+ # 03/01/2007 # UniVec downloaded from NCBI 03/01/2007 [Type] typename : UniVec BLASTN tiername : Contamination datatype : blastn:contam_UniVec glyph : ThinRectangle //glyph : DrawableResultFeatureSet color : 255,0,0 usescore : true column : SCORE column : expect column : identity column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # SEQUENCE | #-----------------------------------------------------------+ # #[Tier] #tiername : sequence #expanded : true #labeled : true # #[Type] #label : sequence #tiername : sequence #datatype : sequence:dummy #glyph : DrawableResultFeatureSet #color : 51,102,255 #usescore : false #column : GENOMIC_RANGE #column : ID #-----------------------------------------------------------+ #-----------------------------------------------------------+ # BEGIN OF COMPUTATIONAL GENE MODEL OUTPUT HERE | #-----------------------------------------------------------+ #-----------------------------------------------------------+ #-----------------------------------------------------------+ # GENSCAN | #-----------------------------------------------------------+ # GENSCAN added 02/14/2007 # Apollo is currently doing something very strange with the # GENSCAN data, it is lumping them into hte GENSCAN-mus # and showing them as a single gene model on the minus # strand. # 04/17/2007 # I did not have the above trouble on the jlb10 machine [Tier] tiername : GENSCAN expanded : true [Type] label : GENSCAN tiername : GENSCAN resulttype : GENSCAN glyph : DrawableResultFeatureSet color : 0,255,0 //usescore : true //minscore : 0.0 //maxscore : 100 column : SCORE column : GENOMIC_RANGE column : query_frame column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # FGENESH | #-----------------------------------------------------------+ [Tier] tiername : Fgenesh expanded : true [Type] label : Fgenesh tiername : Fgenesh resulttype : FGENESH glyph : DrawableResultFeatureSet color : 254,169,90 usescore : true minscore : 0.0 // Need to figure out the best // way to scale the FGENESH results //maxscore : 100 column : SCORE column : GENOMIC_RANGE column : query_frame column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE weburl : http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind# #-----------------------------------------------------------+ # GeneMark.hmm | #-----------------------------------------------------------+ // GeneMark from TriAnnot does not appear to have // score information so he score will be ignored for now. // We may be able to get the score from UGAPAWS. [Tier] tiername : GeneMark.hmm //expanded : true // Will leave combined at the initial open // it can be expanded later to work with the data. expanded : false [Type] typename : GeneMarkHMM_Ta label : GeneMarkHMM Triticum aestivum tiername : GeneMark.hmm resulttype : GeneMarkHMM_Ta glyph : DrawableResultFeatureSet color : 214,187,135 // Commented out score use - 02/08/2007 //usescore : true //minscore : 0.0 column : SCORE column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE [Type] typename : GeneMarkHMM_Hv label : GeneMarkHMM Hordeum vulgare tiername : GeneMark.hmm resulttype : GeneMarkHMM_Hv glyph : DrawableResultFeatureSet color : 216,105,31 //usescore : true //minscore : 0.0 //scorethreshold : -1.0 column : SCORE column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE [Type] typename : GeneMarkHMM_Zm label : GeneMarkHMM Zea Mays tiername : GeneMark.hmm resulttype : GeneMarkHMM_Zm glyph : DrawableResultFeatureSet color : 226,183,37 //usescore : true //minscore : 0.0 //scorethreshold : -1.0 column : SCORE column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE [Type] typename : GeneMarkHMM_Os tiername : GeneMark.hmm resulttype : GeneMarkHMM_Os glyph : DrawableResultFeatureSet color : white //usescore : true //minscore : 0.0 //scorethreshold : -1.0 column : SCORE column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # GeneID | #-----------------------------------------------------------+ [Tier] tiername : geneid expanded : true [Type] typename : geneid_type label : geneid tiername : geneid resulttype : geneid glyph : DrawableResultFeatureSet color : 200,227,98 // Need to add back use score once I figure out the // geneid scoring scheme. //usescore : true //minscore : 0.0 //maxscore : 60 column : SCORE column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # EUGENE | #-----------------------------------------------------------+ [Tier] tiername : eugene expanded : true [Type] typename : eugene_type label : eugene tiername : eugene resulttype : eugene glyph : DrawableResultFeatureSet color : 75,147,216 //usescore : true //minscore : 0.0 column : SCORE column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ #-----------------------------------------------------------+ # BEGIN TE RELATED TIERS HERE #-----------------------------------------------------------+ #-----------------------------------------------------------+ # This is the TEs as drawn for the gene annoation phase of # the project. Folks working on TE annotation may want to # draw these in a more distinguishable way, but the gray # can just be used to represent the masked regions of the # BAC/Genome. # # #-----------------------------------------------------------+ # TRF - Tandem Repeat Finder | #-----------------------------------------------------------+ // Currently not parasing the name from the GFF files from // the TriAnnot web site as I would like [Tier] tiername : RepeatMasker expanded : false [Type] typename : RepeatMasker tiername : TRF datatype : RepeatMasker glyph : DoubleHeadedArrow color : 124,124,124 annot_type : transposable_element //Leaving Name out to see // if this helps the parse of the // name as given in the GFF file //column : NAME column : SCORE column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE [Tier] tiername : TRF expanded : false [Type] label : TRFv4.00 tiername : TRF // TriAnnot used to Use TRF 3.21 // but now appears to be using TRF v4.00 datatype : TRFv3.21 datatype : TRFv4.00 glyph : DoubleHeadedArrow color : 64,64,64 annot_type : transposable_element //Leaving Name out to see // if this helps the parse of the // name as given in the GFF file //column : NAME column : SCORE column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # TREP prot | #-----------------------------------------------------------+ # BLASTX against the TREP protein database [Tier] tiername : TREP prot expanded : false [Type] //label : BLASTX_TREP_prot typename : TREP_prot tiername : TREP prot resulttype : BLASTX_TREP_prot resulttype : blastx:PTREP_9 //glyph : DoubleHeadedArrow glyph : ThinRectangle color : 124,124,124 annot_type : transposable_element column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE // The groupby seems to be ignored // so tryinng to combine the DrawableRestulFeatureSet // with the groupby did not appear to work //groupby : SINGLE weburl : #-----------------------------------------------------------+ # TREP TOTAL | #-----------------------------------------------------------+ # BLASTN AGAINST THE TOTAL TREP REPEAT DATABASE [Tier] tiername : TREP total expanded : false [Type] //label : BLASTN_TREP_total label : TREP_total tiername : TREP total datatype : BLASTN_TREP_total datatype : blastn:TREP9_total glyph : DoubleHeadedArrow color : 84,84,84 annot_type : transposable_element column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE weburl : http://wheat.pw.usda.gov/ITMI/Repeats/Seqfiles.total/__ID__.html #-----------------------------------------------------------+ # TREP nr | #-----------------------------------------------------------+ # BLASTN against the total trep non-redundant databse [Tier] tiername : TREP nr expanded : false [Type] //label : BLASTN_TREP_nr label : TREP_nr tiername : TREP nr datatype : BLASTN_TREP_nr # The following is for local TREP_9 # manually imported into Apollo datatype : blastn:TREP9_nr glyph : DoubleHeadedArrow color : 104,104,104 annot_type : transposable_element # Added query_frame column to see if # this wil allow these to go to the correct query frame //column : query_frame column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE weburl : http://wheat.pw.usda.gov/ITMI/Repeats/Seqfiles.nr/__ID__.html #-----------------------------------------------------------+ # RepBase #-----------------------------------------------------------+ # BLASTN against the RepBase database # Locally this is the RepBase Plants database, I will # need to download the latest version and then hold this # static for the initial GENE annotation phase. [Tier] tiername : RepBase expanded : false [Type] label : RepBase //label : BLASTN_ALL_RepBase tiername : RepBase datatype : BLASTN_ALL_Repbase // The following for manual import of BLAST results datatype : blastn:RB_pln glyph : DoubleHeadedArrow color : 144,144,144 annot_type : transposable_element column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE // TO DO: // Try to draw as a DrawableGeneFeatureSet // with groupby single. // I think this will draw the masked regions as // blocks without trying to join them by exons // RepBase Masked goes here // This may be slightly different then the above due to the // way that the BAC is being masked (WuBLAST or cross_match) // Draw as // 02/08/2007 #-----------------------------------------------------------+ # SanMiguel | #-----------------------------------------------------------+ # BLASTN against the SanMiguel retrotransposon database [Tier] tiername : SanMiguel expanded : false [Type] label : SanMiguel tiername : SanMiguel datatype : BLASTN_SanMiguel // The following added for manual import of local BLAST datatype : blastn:SanMiguel_200610 glyph : DoubleHeadedArrow color : 184,184,184 annot_type : transposable_element column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # MIPS REdat | #-----------------------------------------------------------+ # BLASTN against the MIPS Repetitive Element Database # http://mips.gsf.de/proj/plant/webapp/recat/ # Currently using v. 4.3 of the database # [Tier] tiername : MIPS_REdat expanded : false [Type] label : MIPS REdat 4.3 tiername : MIPS_REdat //datatype : BLASTN_ // The following added for manual import of local BLAST datatype : blastn:mips_REdat_4_3 glyph : DoubleHeadedArrow color : 164,164,164 annot_type : transposable_element column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #weburl : http://mips.gsf.de/proj/plant/webapp/recat/RepeatRetrival.jsp?searchcolumn=name&kw=trep749&coltosort= #weburl : http://mips.gsf.de/proj/plant/webapp/recat/RepeatRetrival.jsp?searchcolumn=name&kw=__ID__&coltosort= # The URL BELOW DOES NOT WORK BECAUSE I USED REPEATMASKER # FORMATTED NAMES weburl : http://mips.gsf.de/proj/plant/webapp/recat/RepeatRetrival.jsp?searchcolumn=name&kw=__ID#__&coltosort= #-----------------------------------------------------------+ # Wessler | #-----------------------------------------------------------+ # BLASTN against the Wessler TE database available from # the MAGI website [Tier] tiername : Wessler expanded : false [Type] label : Wessler tiername : Wessler //datatype : BLASTN_SanMiguel // The following added for manual import of local BLAST datatype : blastn:Wessler glyph : DoubleHeadedArrow //color : 144,144,144 color : 174,174,174 annot_type : transposable_element column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # TriAnnotation Transposons | #-----------------------------------------------------------+ # BlASTN against the CF transposon database # BLASTN against the TriAnnotation provided transposon db [Tier] tiername : Transposon expanded : false [Type] label : TriAnnot_Transposon_BLASTN tiername : Transposon datatype : BLASTN_CF_TRANSPOSON datatype : blastn:TATrans_200702 glyph : DoubleHeadedArrow //color : 124,124,124 color : 184,184,184 annot_type : transposable_element column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # TIGR Gramineae Repeats #-----------------------------------------------------------+ # BLASTN against the TIGR Gramineae repeats # These were downloaded from: # http://www.tigr.org/tdb/e2k1/plant.repeats/ [Tier] tiername : TIGR_Gram_Repeats expanded : false [Type] label : TIGR Gramineae Repeats tiername : TIGR_Gram_Repeats datatype : blastn:TIGR_Gram_3_3 glyph : DoubleHeadedArrow //color : 104,104,104 color : 194,194,194 annot_type : transposable_element column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE # The following url is general for all TIGR Plant repeats # I do not know if specific URLs are available for the databases weburl : http://www.tigr.org/tdb/e2k1/plant.repeats/index.shtml # BLASTN Against Self, I will not be doing this [Type] label : auto blastn tiername : Auto blastn datatype : BLASTN_seq.tfa.db glyph : DoubleHeadedArrow color : 164,164,164 annot_type : transposable_element column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH sortbycolumn : GENOMIC_RANGE #-----------------------------------------------------------+ # Clermont Ferrand mRNA #-----------------------------------------------------------+ # TBLASTX against the Clemont Ferrand mRNA database # This is a track of information that is available from # the TriAnnot pipeline for local BLAST. # I do not know what the nature or source of this data is. [Tier] tiername : Clermont Ferrand mRNA expanded : false [Type] typename : Clermont Ferrand mRNA tiername : Clermont Ferrand mRNA resulttype : TBLASTX_CF_emblPoaRNAc glyph : DrawableResultFeatureSet color : 83,134,213 usescore : true minscore : 0.0 scorethreshold : -1.0 column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false #-----------------------------------------------------------+ #-----------------------------------------------------------+ #-----------------------------------------------------------+ # EST ASSEMBLY SETS | # - NCBI UNIGENES | # - TIGR TAs | # - TIGR GIs | # - Plant GDB PUTs | #-----------------------------------------------------------+ #-----------------------------------------------------------+ #-----------------------------------------------------------+ #-----------------------------------------------------------+ # NCBI UNIGENES | #-----------------------------------------------------------+ # BLASTN against NCBI unigene datasets # The ones availabe from the TriAnnot pipeline include # BLASTN_OS_unigene .......... Oryza sative # BLASTN_WHP_gpi_contigs ..... # I will use the same color scheme by species for the # TIGR GIs and TIGR TAs [Tier] tiername : UniGenes BLASTN expanded : false # Arabidopsis thaliana Unique UniGenes [Type] typename : Arabidopsis thaliana UniGene BLASTN tiername : UniGenes BLASTN resulttype : BLASTN_AT_unigene resulttype : blastn:AtUniGene_56 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Hordeum vulgare Unique UniGenes [Type] typename : Hordeum vulgare UniGene BLASTN tiername : UniGenes BLASTN resulttype : BLASTN_HV_unigene resulttype : blastn:HvUniGene_47 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Oryza sativa Unique Unigenes [Type] typename : Oryza sativa Unigene BLASTN tiername : UniGenes BLASTN resulttype : BLASTN_OS_unigene resulttype : blastn:OsUniGene_65 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Sorghum bicolor Unique UniGenes [Type] typename : Sorghum bicolor UniGene BLASTN tiername : UniGenes BLASTN resulttype : blastn:SbUniGene_21 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Saccharum Unique UniGenes [Type] typename : Saccharum officinarum UniGene BLASTN tiername : UniGenes BLASTN resulttype : blastn:SoUniGene_8 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Triticum aestivum Unique Unigene [Type] typename : Triticum aestivum UniGene BLASTN tiername : UniGenes BLASTN resulttype : BLASTN_TA_unigene resulttype : blastn:TaUniGene_46 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false #weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ #weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?CID=__ID.__ # Zea mays Unique UniGene [Type] typename : Zea mays UniGene BLASTN tiername : UniGenes BLASTN resulttype : BLASTN_ZM_unigene resulttype : blastn:ZmUniGene_61 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ #-----------------------------------------------------------+ # NCBI UNIGENES TBLASTX | #-----------------------------------------------------------+ # TO DO: ADD ALL UNIGENES HERE [Tier] tiername : UniGenes TBLASTX expanded : false # Arabidopsis thaliana Unique UniGenes [Type] typename : Arabidopsis thaliana UniGene TBLASTX tiername : UniGenes TBLASTX resulttype : BLASTN_AT_unigene resulttype : blastx:AtUniGene_56 resulttype : tblastx:AtUniGene_56 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Hordeum vulgare Unique UniGenes [Type] typename : Hordeum vulgare UniGene_TBLASTX tiername : UniGenes TBLASTX resulttype : BLASTN_HV_unigene resulttype : blastx:HvUniGene_47 resulttype : tblastx:HvUniGene_47 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Oryza sativa Unique Unigenes [Type] typename : Oryza sativa Unigene TBLASTX tiername : UniGenes TBLASTX resulttype : BLASTN_OS_unigene resulttype : blastx:OsUniGene_65 resulttype : tblastx:OsUniGene_65 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Sorghum bicolor Unique UniGenes [Type] typename : Sorghum bicolor UniGene TBLASTX tiername : UniGenes TBLASTX resulttype : blastx:SbUniGene_21 resulttype : tblastx:SbUniGene_21 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Saccharum Unique UniGenes [Type] typename : Saccharum officinarum UniGene TBLASTX tiername : UniGenes TBLASTX resulttype : blastx:SoUniGene_8 resulttype : tblastx:SoUniGene_8 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ # Triticum aestivum Unique Unigene [Type] typename : Triticum aestivum UniGene TBLASTX tiername : UniGenes TBLASTX resulttype : BLASTN_TA_unigene resulttype : blastx:TaUniGene_46 resulttype : tblastx:TaUniGene_46 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/seq.cgi?ORG=__ID#__&SID=__ID__ # Zea mays Unique UniGene [Type] typename : Zea mays UniGene TBLASTX tiername : UniGenes TBLASTX resulttype : BLASTN_ZM_unigene resulttype : blastx:ZmUniGene_61 resulttype : tblastx:ZmUniGene_61 glyph : DrawableResultFeatureSet color : red usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=__ID.__&CID=__ID__ #-----------------------------------------------------------+ # TIGR GIs BLASTN #-----------------------------------------------------------+ # GIs are from the TIGR Gene Index database: # I believe that this has largely been replaced by the # TIGR TAs but I will need to take a look at these for # at least 10 BACs to be sure. # -- JCE 02/14/2007 # MAY want to switc to a BLASTN search for the TaGI # while all others get the tBLASTx treatment # THESE ARE CURRENTLY ALL IN BLUE # THIS SHOULD PROBABLY BE CHANGED [Tier] tiername : TIGR GIs BLASTN expanded : false # The following is currently a BLASTN # search, this may need to be replaced # by a TBLASTX, However since these are # from T. aestivum may be able to just # stick with BLASTn # Show this is yellow [Type] typename : Arabidopsis thaliana GI BLASTN tiername : TIGR GIs BLASTN resulttype : blastn:AtGI_13 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Hordeum vulgare GI BLASTN tiername : TIGR GIs BLASTN resulttype : blastn:HvGI_9 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Oryza sativa GI BLASTN tiername : TIGR GIs BLASTN resulttype : blastn:OsGI_17 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Sorghum bicolor GI BLASTN tiername : TIGR GIs BLASTN resulttype : blastn:SbGI_9 resulttype : blastn:SbGI_8 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Triticum aestivum GI BLASTN tiername : TIGR GIs BLASTN resulttype : blastn:TaGI_10 //resulttype : TBLASTX_TA_tigrta glyph : DrawableResultFeatureSet //color : 255,255,0 // BLUE color : 0,0,255 //commented out score 02/08/2007 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Zea mays GI BLASTN tiername : TIGR GIs BLASTN resulttype : blastn:ZmGI_17 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false #-----------------------------------------------------------+ # TIGR GIs TBLASTX #-----------------------------------------------------------+ [Tier] tiername : TIGR GIs TBLASTX expanded : false # The following is currently a BLASTN # search, this may need to be replaced # by a TBLASTX, However since these are # from T. aestivum may be able to just # stick with BLASTn # Show this is yellow [Type] typename : Arabidopsis thaliana GI TBLASTX tiername : TIGR GIs TBLASTX resulttype : blastx:AtGI_13 resulttype : tblastx:AtGI_13 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Hordeum vulgare GI TBLASTX tiername : TIGR GIs TBLASTX resulttype : blastx:HvGI_9 resulttype : tblastx:HvGI_9 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Oryza sativa GI TBLASTX tiername : TIGR GIs TBLASTX resulttype : blastx:OsGI_17 resulttype : tblastx:OsGI_17 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Sorghum bicolor GI TBLASTX tiername : TIGR GIs TBLASTX resulttype : blastx:SbGI_9 resulttype : tblastx:SbGI_9 resulttype : blastx:SbGI_8 resulttype : tblastx:SbGI_8 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Triticum aestivum GI TBLASTX tiername : TIGR GIs TBLASTX resulttype : blastx:TaGI_10 resulttype : tblastx:TaGI_10 resulttype : TBLASTX_TA_tigrta glyph : DrawableResultFeatureSet //color : 255,255,0 color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false [Type] typename : Zea mays GI TBLASTX tiername : TIGR GIs TBLASTX resulttype : blastx:ZmGI_17 resulttype : tblastx:ZmGI_17 glyph : DrawableResultFeatureSet color : 0,0,255 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false #-----------------------------------------------------------+ # TIGR TAs BLASTN | #-----------------------------------------------------------+ # TAs are TIGR transcript assemblies: # These may or may not be redundant with the TGI # TIGR Gene Indices and may or may not be redundant # with the NCBI unigenes. # Either way I should add the following TIERS for evaluation # by the ateam group. # TAS may be downloaded from # ftp://ftp.tigr.org/pub/data/plantta/ [Tier] tiername : TIGR TAs BLASTN expanded : false [Type] typename : Agrostis capillaris TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:AcTA_1 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Agrostis stolonifera TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:AsTA_1 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : score column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Arabidopsis thaliana TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:AtTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Avena sativa TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:AvenSatTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Cynodon dactylon TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:CdTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Festuca arundinaceae TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:FaTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Hordeum vulgare TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:HvTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Oryza sativa TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:OsTA_2 resulttype : blastn:OsTA2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Pennistum glaucum TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:PgTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Saccharum officinarum TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:SoTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Sorghum bicolor TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:SbTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Sorghum halepense TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:ShTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Sorghum propinquum TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:SpTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Triticum aestivum TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:TaTA_2 glyph : DrawableResultFeatureSet color : 212,76,99 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE //weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta=TA67744_4530 weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Triticum monococcum Tas tiername : TIGR TAs BLASTN resulttype : TBLASTX_TM_tigrta resulttype : blastn:TmTA_2 glyph : DrawableResultFeatureSet color : 230,180,96 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Triticum turgidum Tas tiername : TIGR TAs BLASTN resulttype : TBLASTX_TT_tigrta resulttype : blastn:TtTa_1 glyph : DrawableResultFeatureSet color : 163,100,38 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Zea mays B73 TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:ZmB73TA_1 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Zea mays TAs BLASTN tiername : TIGR TAs BLASTN resulttype : blastn:ZmTA_3 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= # MAY WANT TO GET AEGILOPS # I don't think I have this one [Type] typename : Aegilops tauschii Tas tiername : TIGR TAs BLASTN resulttype : TBLASTX_AS_tigrta glyph : DrawableResultFeatureSet color : 178,139,57 //commented out score //usescore : true //minscore : 0.0 //scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= # DO THE BLASTX HERE FOR TIGR TAs #-----------------------------------------------------------+ # TIGR TAs TBLASTX #-----------------------------------------------------------+ # BLASTX allows for the direction of the sequence when # importing into Apollo [Tier] tiername : TIGR TAs TBLASTX expanded : false [Type] typename : Agrostis capillaris TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:AcTA_1 resulttype : tblastx:AcTA_1 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Agrostis stolonifera TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:AsTA_1 resulttype : tblastx:AsTA_1 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Arabidopsis thaliana TAs TBLASTNX tiername : TIGR TAs TBLASTX resulttype : blastx:AtTA_2 resulttype : tblastx:AtTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Avena sativa TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:AvenSatTA_2 resulttype : tblastx:AvenSatTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Cynodon dactylon TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:CdTA_2 resulttype : tblastx:CdTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Festuca arundinaceae TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:FaTA_2 resulttype : tblastx:FaTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Hordeum vulgare TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:HvTA_2 resulttype : tblastx:HvTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Oryza sativa TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:OsTA_2 resulttype : blastx:OsTA2 resulttype : tblastx:OsTA_2 resulttype : tblastx:OsTA2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Pennistum glaucum TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:PgTA_2 resulttype : tblastx:PgTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Saccharum officinarum TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:SoTA_2 resulttype : tblastx:SoTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Sorghum bicolor TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:SbTA_2 resulttype : tblastx:SbTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Sorghum halepense TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:ShTA_2 resulttype : tblastx:ShTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Sorghum propinquum TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:SpTA_2 resulttype : tblastx:SpTA_2 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Triticum aestivum TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : TBLASTX_TA_tigrta resulttype : blastx:TaTA_2 resulttype : tblastx:TaTA_2 glyph : DrawableResultFeatureSet color : 212,76,99 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Triticum monococcum TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : TBLASTX_TM_tigrta resulttype : blastx:TmTA_2 resulttype : tblastx:TmTA_2 glyph : DrawableResultFeatureSet color : 230,180,96 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Triticum turgidum TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : TBLASTX_TT_tigrta resulttype : blastx:TtTa_1 resulttype : tblastx:TtTa_1 glyph : DrawableResultFeatureSet color : 163,100,38 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Zea mays B73 TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:ZmB73TA_1 resulttype : tblastx:ZmB73TA_1 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= [Type] typename : Zea mays TAs TBLASTX tiername : TIGR TAs TBLASTX resulttype : blastx:ZmTA_3 resulttype : tblastx:ZmTA_3 glyph : DrawableResultFeatureSet //color : 212,76,99 color : yellow usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://plantta.tigr.org/cgi-bin/plantta_report.pl?ta= #-----------------------------------------------------------+ # Plant GDB PUTs BLASTN #-----------------------------------------------------------+ # Partial list for today 02/20/2007 # This needs to be finished for all potential PUTs [Tier] tiername : PlantGDB PUTs BLASTN expanded : false [Type] typename : Hordeum vulgare PUTs BLAST tiername : PlantGDB PUTs BLASTN resulttype : blastn:HvPUT_157 glyph : DrawableResultFeatureSet //color : 212,76,99 color : 0,255,0 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false # WEB URL SOMETHING LIKE # http://www.plantgdb.org/search/display/data.php?Seq_ID=PUT-151a-Hordeum_vulgare-1535106207 # This may work with something like #http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ weburl : http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ [Type] typename : Triticum aestivum PUTs BLASTN tiername : PlantGDB PUTs BLASTN resulttype : blastn:TaPUT_157 glyph : DrawableResultFeatureSet //color : 212,76,99 color : 0,255,0 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ // May want to split the following into // finer groups [Type] typename : POACEAE PUTs BLASTN tiername : PlantGDB PUTs BLASTN resulttype : blastn:OsIndPUT_157 resulttype : blastn:OsJapPUT_157 resulttype : blastn:OsPUT_157 resulttype : blastn:TmPUT_157 resulttype : blastn:SbPUT_157 glyph : DrawableResultFeatureSet //color : 212,76,99 color : 0,255,0 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ #-----------------------------------------------------------+ # Plant GDB PUTS TBLASTS | #-----------------------------------------------------------+ # Partial list for today 02/20/2007 # This needs to be finished for all potential PUTs [Tier] tiername : PlantGDB PUTs TBLASTX expanded : false // MAY WANT TO SPLIT THE FOLLOWING // TO A FINER DETAIL [Type] typename : Poaceae PUTs TBLASTX tiername : PlantGDB PUTs TBLASTX resulttype : blastx:OsIndPUT_157 resulttype : blastx:SpPut_157 resulttype : blastx:OsJapPUT_157 resulttype : blastx:OsZmPUT_157 resulttype : blastx:OsIndPUT_157 resulttype : blastx:AtPUT_157 resulttype : blastx:AsPUT_157 resulttype : blastx:ZmPUT_157 resulttype : tblastx:OsIndPUT_157 resulttype : tblastx:SpPut_157 resulttype : tblastx:OsJapPUT_157 resulttype : tblastx:OsZmPUT_157 resulttype : tblastx:OsIndPUT_157 resulttype : tblastx:AtPUT_157 resulttype : tblastx:AsPUT_157 resulttype : tblastx:ZmPUT_157 glyph : DrawableResultFeatureSet //color : 212,76,99 color : 102,255,102 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ [Type] typename : Hordeum vulgare PUTs TBLASTX tiername : PlantGDB PUTs TBLASTX resulttype : blastx:HvPUT_157 resulttype : tblastx:HvPUT_157 glyph : DrawableResultFeatureSet //color : 212,76,99 color : 102,255,102 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ [Type] typename : Triticum aestivum PUTs TBLASTX tiername : PlantGDB PUTs TBLASTX resulttype : blastx:TaPUT_157 resulttype : tblastx:TaPUT_157 glyph : DrawableResultFeatureSet //color : 212,76,99 color : 102,255,102 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ [Type] typename : Triticum monococcum PUTs TBLASTX tiername : PlantGDB PUTs TBLASTX resulttype : blastx:TmPUT_157 resulttype : tblastx:TmPUT_157 glyph : DrawableResultFeatureSet //color : 212,76,99 color : 102,255,102 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ [Type] typename : Oryza sativa PUTs TBLASTX tiername : PlantGDB PUTs TBLASTX resulttype : blastx:OsPUT_157 resulttype : tblastx:OsPUT_157 glyph : DrawableResultFeatureSet //color : 212,76,99 color : 102,255,102 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ [Type] typename : Sorghum bicolor PUTs TBLASTX tiername : PlantGDB PUTs TBLASTX resulttype : blastx:SbPUT_157 resulttype : tblastx:SbPUT_157 glyph : DrawableResultFeatureSet //color : 212,76,99 color : 102,255,102 usescore : true minscore : 0.0 scorethreshold : -1.0 column : SCORE column : expect column : identity column : GENOMIC_RANGE column : GENOMIC_LENGTH column : MATCH_RANGE reversesort : false weburl : http://www.plantgdb.org/search/display/data.php?Seq_ID=__ID#__ # JAMIE COMMENTED OUT THE FOLLOWING 02/20/2007 ##-----------------------------------------------------------+ ## EST | ##-----------------------------------------------------------+ ## BLASTN against EST databases #[Tier] #tiername : EST #expanded : false # #[Type] #typename : BLASTN_OS_CDS #label : TIGR oryza sativa CDS prediction #tiername : CDS #datatype : BLASTN_OS_CDS #glyph : DrawableResultFeatureSet #color : 255,255,255 #//usescore : true #column : NAME #column : SCORE #column : GENOMIC_RANGE #column : MATCH_RANGE #column : GENOMIC_LENGTH #column : MATCH_LENGTH #sortbycolumn : GENOMIC_RANGE #groupby : HOMOLOGY # #[Type] #typename : BLASTN_embl_est_pln #label : EST other #tiername : EST #datatype : BLASTN_embl_est_pln #glyph : DrawableResultFeatureSet #color : 102,255,102 #//usescore : true #column : NAME #column : SCORE #column : GENOMIC_RANGE #column : MATCH_RANGE #column : GENOMIC_LENGTH #column : MATCH_LENGTH #sortbycolumn : GENOMIC_RANGE #groupby : HOMOLOGY # #-----------------------------------------------------------+ # EMBL BLASTX | #-----------------------------------------------------------+ # Tier Added : 02/20/2007 # May also need to consider just doing the BLASTP from the # predicted gene models if this is way to slow. However # I can just farm this BLAST out to the IOB cluster. # The data I retrieve is indexed by the primaryAc identifier # MAY WANT TO ADD EMBL_CDS # ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/README.txt [Tier] tiername : EMBL UniProt (BLASTX) expanded : false [Type] label : UniProt Swiss-Prot (BLASTX) tiername : EMBL UniProt (BLASTX) datatype : blastx:UniProt_SProt_34_7 glyph : DrawableResultFeatureSet color : 255,20,0 usescore : true column : SCORE column : expect column : identity column : query_frame column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE groupby : HOMOLOGY weburl : http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?primaryAc= [Type] label : UniProt TrEMBL (BLASTX) tiername : EMBL UniProt (BLASTX) datatype : blastx:UniProt_TrEMBL_34_7 glyph : DrawableResultFeatureSet color : 200,20,0 usescore : true column : SCORE column : expect column : identity column : query_frame column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE groupby : HOMOLOGY weburl : http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?primaryAc= #-----------------------------------------------------------+ # sim4 #-----------------------------------------------------------+ # Added 02/24/2007 # Program Source: http://www.bx.psu.edu/miller_lab/ # Pub: http://www.genome.org/cgi/content/full/8/9/967 # The sim4 program should be run against the mRNA information # from T. aestivum ##-----------------------------------------------------------+ ## genomic homoloies ##-----------------------------------------------------------+ ## Unclear as to what this is # #[Tier] #tiername : genomic homologies #expanded : false # #[Type] #typename : BLASTN_CF_bac #label : local BACdb #tiername : genomic homologies #datatype : BLASTN_CF_bac #glyph : DrawableResultFeatureSet #color : 239,130,031 #//usescore : true #column : NAME #column : SCORE #column : GENOMIC_RANGE #column : MATCH_RANGE #column : GENOMIC_LENGTH #column : MATCH_LENGTH #sortbycolumn : GENOMIC_RANGE #groupby : HOMOLOGY # #[Type] #typename : BLASTN_embl_gss_pln #label : PLN GSS #tiername : genomic homologies #datatype : BLASTN_embl_gss_pln #glyph : DrawableResultFeatureSet #color : 239,130,031 #usescore : true #column : NAME #column : SCORE #column : GENOMIC_RANGE #column : MATCH_RANGE #column : GENOMIC_LENGTH #column : MATCH_LENGTH #sortbycolumn : GENOMIC_RANGE #groupby : HOMOLOGY # #[Type] #typename : BLASTN_Embl_htg_pln #label : PLN HTG #tiername : genomic homologies #datatype : BLASTN_Embl_HTG_PLN #glyph : DrawableResultFeatureSet #color : 239,130,031 #//usescore : true #column : NAME #column : SCORE #column : GENOMIC_RANGE #column : MATCH_RANGE #column : GENOMIC_LENGTH #column : MATCH_LENGTH #sortbycolumn : GENOMIC_RANGE #groupby : HOMOLOGY ##-----------------------------------------------------------+ ## STS ##-----------------------------------------------------------+ # #[Tier] #tiername : STS #expanded : false # #[Type] #typename : BLASTN_embl_sts_pln #label : STS #tiername : STS #datatype : BLASTN_embl_sts_pln #glyph : DrawableResultFeatureSet #color : 102,255,102 #//usescore : true #column : NAME #column : SCORE #column : GENOMIC_RANGE #column : MATCH_RANGE #column : GENOMIC_LENGTH #column : MATCH_LENGTH #sortbycolumn : GENOMIC_RANGE #groupby : HOMOLOGY # ##-----------------------------------------------------------+ ## other_homologies ##-----------------------------------------------------------+ # #[Tier] #tiername : other homologies #expanded : false # #[Type] #typename : BLASTN_Embl_PLN #label : EMBL #tiername : other homologies #datatype : BLASTN_Embl_PLN #glyph : DrawableResultFeatureSet #color : 102,255,102 #//usescore : true #column : NAME #column : SCORE #column : GENOMIC_RANGE #column : MATCH_RANGE #column : GENOMIC_LENGTH #column : MATCH_LENGTH #sortbycolumn : GENOMIC_RANGE #groupby : HOMOLOGY #-----------------------------------------------------------+ # CDS BLASTX ARABIDOPSIS | #-----------------------------------------------------------+ [Tier] tiername : CDS Arabidopsis expanded : false #-----------------------------+ # TAIR V 6 | # 03/01/2007 | #-----------------------------+ [Type] typename : Arabidopsis CDS BLASTX tiername : CDS Arabidopsis datatype : blastx:TAIR6 glyph : DrawableResultFeatureSet color : 255,0,0 usescore : true column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE groupby : HOMOLOGY // The following is redundant with TAIR // TAIR seems to be the better model [Type] typename : Arabidopsis CDS TBLASTX (TIGR) tiername : CDS Arabidopsis datatype : blastx:ATH1_cds glyph : DrawableResultFeatureSet color : 255,0,0 usescore : true column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE groupby : HOMOLOGY #-----------------------------------------------------------+ # PROTEIN MODEL (CDS) BLASTX | #-----------------------------------------------------------+ # Should add putative transposon to this tier under # the fly.type preferences [Tier] tiername : CDS Rice TIGR expanded : false [Type] typename : Rice CDS BLASTX tiername : CDS Rice TIGR datatype : blastx:Os_5_cds_pep glyph : DrawableResultFeatureSet color : 20,255,20 usescore : true column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE groupby : HOMOLOGY // The following is really redundant // but left here for the DirtyDozen [Type] typename : Rice CDS TBLASTX tiername : CDS Rice TIGR datatype : blastx:Os_5_cds datatype : tblastx:Os_5_cds glyph : DrawableResultFeatureSet color : 20,255,20 usescore : true column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE groupby : HOMOLOGY [Tier] tiername : CDS BLASTN Rice TIGR expanded : false // The following is really redundant // but left here for the DirtyDozen [Type] typename : Rice CDS BLASTN tiername : CDS BLASTN Rice TIGR datatype : blastn:Os_5_cds glyph : DrawableResultFeatureSet color : 20,255,20 usescore : true column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE groupby : HOMOLOGY #-----------------------------------------------------------+ # PROTEIN MODEL (CDS) RAP 1 | # http://rapdownload.lab.nig.ac.jp/ | #-----------------------------------------------------------+ [Tier] tiername : CDS RICE RAP1 expanded : false [Type] typename : Rice CDS BLASTX tiername : CDS Rice RAP1 // The _pe is a problem with the database on an early version // of the DAWG-PAWS pipeline datatype : blastx:Os_Rap1_pep datatype : blastx:Os_Rap1_pe glyph : DrawableResultFeatureSet color : 255,255,255 usescore : true column : NAME column : SCORE column : expect column : identity column : GENOMIC_RANGE column : MATCH_RANGE column : GENOMIC_LENGTH column : MATCH_LENGTH sortbycolumn : GENOMIC_RANGE groupby : HOMOLOGY weburl : http://rapdownload.lab.nig.ac.jp/