178	<a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/27/2/573?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Benson&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;fdate=1/1/1999&amp;tdate=12/31/1999&amp;resourcetype=HWCIT">Tandem Repeats Finder</a> locates adjacent copies of a pattern of nucleotides.	Tandem repeats (TRF)	1	\N
177	Dust is a program that identifies low-complexity sequences (regions of the genome with a biased distribution of nucleotides, such as a repeat). The Dust module is widely used with BLAST to prevent 'sticky' regions from determining false hits.	Low complexity (Dust)	1	\N
101	<a href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a> alignments (coverage >=95%, %id >= 94%) of predicted ORFs assembled from <i>Triticum aestivum</i> (bread wheat) public datasets. Supplied by <a href="http://www.tgac.ac.uk">The Center for Genome Analysis</a> as part of the <a href="http://maswheat.ucdavis.edu/Transcriptome/">Triticeae-CAP</a> project. Published as supplemental dataset 7, in <a href="http://genomebiology.com/content/14/6/R66">Krasileva et al.</a>, PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/23800085">23800085</a>.	T. aestivum RNA-seq alignment	1	{'label_key':'[biotype]', colour_key:'[biotype]', 'default':{'MultiTop':'gene_label', 'contigviewbottom':'transcript_label', 'MultiBottom':'collapsed_label', 'contigviewtop':'gene_label', 'cytoview':'gene_label', 'alignsliceviewbottom':'as_collapsed_label' }, name:'T. aestivum RNA-seq alignments', caption:'T. aestivum RNA-seq alignments', multi_name:'T. aestivum RNA-seq alignments'}
186	HMM-Panther families	PANTHER	1	{'type':'domain'}
195	Prediction of coiled-coil regions in proteins is by <a rel="external" href="http://www.sciencemag.org/cgi/reprint/252/5009/1162">Ncoils</a>.	Coiled-coils (Ncoils)	1	\N
184	Gene3D analysis as of interpro_scan.pl	Gene3D	1	{'type':'domain'}
188	Protein domains and motifs from the <a rel="external" href="http://www.ebi.ac.uk/ppsearch/">PROSITE</a> profiles database are aligned to the genome.	PROSITE profiles	1	{'type':'domain'}
198	Identification of peptide low complexity sequences by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6TFV-44PXMF3-45&amp;_user=776054&amp;_coverDate=06%2F30%2F1993&amp;_rdoc=6&amp;_fmt=high&amp;_orig=browse&amp;_srch=doc-info(%23toc%235236%231993%23999829997%23279143%23FLP%23display%23Volume)&amp;_cdi=5236&amp;_sort=d&amp;_docanchor=&amp;_ct=13&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;md5=ac6f98882f2c6626643118367fb28cad">Seg</a>.	Low complexity (Seg)	1	\N
187	Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D138?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Bateman&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;resourcetype=HWCIT">Pfam</a> database.	Pfam	1	{'type':'domain'}
190	Protein fingerprints (groups of conserved motifs) are aligned to the genome. These motifs come from the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/abstract/31/1/400?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Attwood&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;resourcetype=HWCIT">PRINTS</a> database.	Prints	1	{'type':'domain'}
183	NCBI-BlastP search against ProDom families	ProDom	1	{'type':'domain'}
189	Protein domains and motifs from the <a rel="external" href="http://pir.georgetown.edu/pirwww/index.shtml">PIR (Protein Information Resource)</a> Superfamily database.	PIRSF	1	{'type':'domain'}
185	HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins	HAMAP	1	{'type':'domain'}
192	Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D257?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=letunic&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;fdate=1/1/2006&amp;tdate=12/31/2006&amp;resourcetype=HWCIT">SMART</a> database.	SMART	1	{'type':'domain'}
197	Prediction of transmembrane helices in proteins by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WK7-457D7V9-K&amp;_user=776054&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;md5=a113464457fa5206c6699b9d464cbfee">TMHMM</a>.	Transmembrane helices	1	\N
191	Protein domains and motifs from the <a rel="external" href="http://www.ebi.ac.uk/ppsearch/">PROSITE</a> profiles database are aligned to the genome.	PROSITE patterns	1	{'type':'domain'}
196	Prediction of signal peptide cleavage sites by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WK7-4CKBS0M-3&amp;_user=776054&amp;_coverDate=07%2F16%2F2004&amp;_alid=772330061&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_cdi=6899&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_ct=1&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;md5=9f42be939814b7711268fd414604c9dd">SignalP</a>.	Cleavage site (Signalp)	1	{'type':'feature'}
200	InterPro2Pathway mapping is obtained from interproScan results.	InterPro2Pathway mapping	1	\N
194	Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/31/1/371?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Haft&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;fdate=1/1/2003&amp;tdate=12/31/2003&amp;resourcetype=HWCIT">TIGRFAM</a> database.	TIGRFAM	1	{'type':'domain'}
119	<i>Triticum aestivum</i> genes annotated by <a href="http://mips.helmholtz-muenchen.de/plant/wheat/">MIPS</a>	MIPS	1	{'colour_key':'[biotype]', 'label_key':'[biotype]','default':{'MultiTop':'gene_label','contigviewbottom':'transcript_label','MultiBottom':'collapsed_label','contigviewtop':'gene_label','alignsliceviewbottom':'as_collapsed_label','cytoview':'gene_label'}, 'name':'Protein-coding Gene (MIPS)', 'caption':'Protein-coding Gene (MIPS)', 'multi_name':'Protein-coding Gene (MIPS)','key':'ensembl'}
45	<i>T. aestivum</i> Inter-homoeologous Variants that differ between the A and D genomes (where the B genome is unknown)	Brenchley et al. T. aestivum Genome A/D SNPs	1	\N
46	<i>T. aestivum</i> Inter-homoeologous Variants that are the same between the A and D genomes, but differ in B	Brenchley et al. T. aestivum Genome B SNPs	1	\N
136	Sequences from various databases are matched to Ensembl transcripts using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. These are external references, or "Xrefs".	DNA match	0	\N
137	match	Protein	0	\N
138	Xref mapping based on checksum equivalency	Xref checksum	0	\N
100	<a href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a> alignments (coverage >=95%, %id >= 94%) of predicted ORFs assembled from <i>Triticum turgidum</i> (durum wheat) RNA-seq. Supplied by <a href="http://www.tgac.ac.uk">The Center for Genome Analysis</a> as part of the <a href="http://maswheat.ucdavis.edu/Transcriptome/">Triticeae-CAP</a> project. Published as supplemental dataset 7, in <a href="http://genomebiology.com/content/14/6/R66">Krasileva et al.</a>, PMID:<a href="http://www.ncbi.nlm.nih.gov/pubmed/23800085">23800085</a>.	T. turgidum RNA-seq alignment	1	{'label_key':'[biotype]', colour_key:'[biotype]', 'default':{'MultiTop':'gene_label', 'contigviewbottom':'transcript_label', 'MultiBottom':'collapsed_label', 'contigviewtop':'gene_label', 'cytoview':'gene_label', 'alignsliceviewbottom':'as_collapsed_label' }, name:'T. turgidum RNA-seq alignments', caption:'T. turgidum RNA-seq alignments', multi_name:'T. turgidum RNA-seq alignments)'}
140	ncRNA genes are predicted using a combination of methods depending on their type. tRNAs are predicted using <a href="http://selab.janelia.org/tRNAscan-SE/">tRNAScan-SE</a>, rRNAs using <a href="http://www.cbs.dtu.dk/services/RNAmmer/">RNAmmer</a>, and for all other types, using covariance models and sequences from <a href="http://rfam.sanger.ac.uk/">RFAM</a>.	ncRNA	1	{'colour_key':'[biotype]','caption':'ncRNA','label_key':'[biotype]','name':'ncRNA','default':{'contigviewbottom' =>'transcript_label','contigviewtop':'gene_label','cytoview':'gene_label'},'key':'ncRNA'}
141	Protein coding genes annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a>	Protein coding genes (ENA)	1	{'colour_key':'[biotype]','caption':'Genes','name':'Genes','label_key':'[biotype]','default':{'MultiTop':'gene_label','contigviewbottom':'transcript_label','MultiBottom':'collapsed_label','contigviewtop':'gene_label','cytoview':'gene_label','alignsliceviewbottom':'as_collapsed_label'},'multi_caption':'Genes','key':'ena_genes'}
142	Cross-references attached by GenomeLoader	GenomeLoader cross-references	1	\N
143	Cross-references attached by GenomeLoader to provide names	GenomeLoader name cross-references	1	\N
145	ncRNA genes annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a>	ncRNA genes (ENA)	1	{'colour_key':'[biotype]','caption':'Genes','name':'Genes','label_key':'[biotype]','default':{'MultiTop':'gene_label','contigviewbottom':'transcript_label','MultiBottom':'collapsed_label','contigviewtop':'gene_label','cytoview':'gene_label','alignsliceviewbottom':'as_collapsed_label'},'multi_caption':'Genes','key':'ena_genes'}
146	gene feature annotated in ENA	gene (ENA)	1	{'multi_name':'Genomic features','caption':'Genomic features','name':'Genomic features','label_key':'[text_label] [display_label]','key':'ena_features'}
147	exon feature annotated in ENA	exon (ENA)	1	{'multi_name':'Genomic features','caption':'Genomic features','name':'Genomic features','label_key':'[text_label] [display_label]','key':'ena_features'}
148	Percentage of G/C bases in the sequence.	GC content	1	\N
149	Long non-coding gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Production/Pipeline/Production/NonCodingDensity.pm?root=ensembl&view=markup">LongNonCodingDensity.pm</a>.	Long non-coding genes (density)	1	\N
150	Pseudogene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Pipeline/Production/PseudogeneDensity.pm?root=ensembl&view=markup">PseudogeneDensity.pm</a>.	Pseudogenes (density)	1	\N
151	Short non-coding gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Production/Pipeline/Production/NonCodingDensity.pm?root=ensembl&view=markup">ShortNonCodingDensity.pm</a>.	Short non-coding genes (density)	1	\N
152	Coding gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Pipeline/Production/CodingDensity.pm?root=ensembl&view=markup">CodingDensity.pm</a>.	Coding genes (density)	1	\N
153	Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.)	Repeats (percent)	1	\N
154	Repeat regions annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a>	Repeats (ENA)	1	\N
155	Direct repeat regions annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a>	Direct repeats (ENA)	1	\N
156	Density of single nucleotide polymorphisms (SNPs) as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Pipeline/Production/SnpDensity.pm?root=ensembl&view=markup">SNPDensity.pm</a>.	SNP Density	1	\N
157	The XRef projection pipeline re-implemented by CK based on work by Andy and tweaked by Dan	Projected XRef	0	\N
199	InterPro2GO file is generated manually by the InterPro team at the EBI.	InterPro2GO mapping	1	\N
193	Protein domains and motifs in the <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WK7-457CXWM-3D&amp;_user=776054&amp;_coverDate=11%2F02%2F2001&amp;_rdoc=17&amp;_fmt=high&amp;_orig=browse&amp;_srch=doc-info(%23toc%236899%232001%23996869995%23286382%23FLA%23display%23Volume)&amp;_cdi=6899&amp;_sort=d&amp;_docanchor=&amp;_ct=17&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;md5=a921e84cd71c59f75644aa28f3224b58">SUPERFAMILY</a> database.	Superfamily	1	{'type':'domain'}
176	<i>Triticum aestivum</i> 3B chromosome genes annotated by <a href="http://www6.clermont.inra.fr/umr1095_eng">INRA GDEC group</a>	GDEC 3B annotation	1	{'colour_key':'[biotype]', 'label_key':'[biotype]','default':{'MultiTop':'gene_label','contigviewbottom':'transcript_label','MultiBottom':'collapsed_label','contigviewtop':'gene_label','alignsliceviewbottom':'as_collapsed_label','cytoview':'gene_label'}, 'name':'GDEC', 'caption':'GDEC', 'multi_name' =>'GDEC','key':'gdec'}
180	<a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> is used to find repeats and low-complexity sequences. This track usually shows repeats alone (not low-complexity sequences).	Repeats	1	\N
181	Repeats detected using the <a href="http://wheat.pw.usda.gov/ITMI/Repeats/">TREP</a> library (trep.nr) using <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a>.	Repeats TREP library	1	\N
