From 39b2b36168414be66c3c8c715fd673cb4e3119d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 15 Oct 2008 08:00:49 +0000
Subject: [PATCH] The entry for 'probe2Transcript' was not tab-delimited
properly.
Removed empty line.
Removed trailing spaces.
---
.../analysis.descriptions | 33 +++++++++----------
1 file changed, 16 insertions(+), 17 deletions(-)
diff --git a/misc-scripts/analysis_description/analysis.descriptions b/misc-scripts/analysis_description/analysis.descriptions
index 1c6be12da1..872f985ba0 100644
--- a/misc-scripts/analysis_description/analysis.descriptions
+++ b/misc-scripts/analysis_description/analysis.descriptions
@@ -1,17 +1,17 @@
# Note fields in this file should be separated by *tabs* not spaces!
#
-# format: nr<TAB>logic_name<TAB>display_label<TAB>description
+# format: nr<TAB>logic_name<TAB>display_label<TAB>description
#
1 Ab_initio_RepeatMask Repeats Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using ab initio repeat profiles specific to the species.
1 AlignAffy Probes (Affymetrix) Microarray probes from Affymetrix are aligned to the genome by Ensembl, if probe sequences are provided. These genomic mapping are then used as the input for the transcript mapping process outlined <a href="/htdocs/info/docs/microarray_probe_set_mapping.html">here</a>.
-1 probe2Transcript Microarray Probe Sets Ensembl annotates microarray probe sets on the genome sequences if manufacturers disclosed individual probe set sequences for a particular micro array. The Ensembl 'ContigView' displays probes that match to the current assembly. If not displayed by default, microarray probe set tracks are available from the 'Features' menu in the yellow menu bar of the 'Detailed View' panel. Pointing at a particular probe in a probe set track displays a pop-up window which links to the probe set details on the FeatureView page. Here a karyotype image is annotated with probe locations accompanied by a table listing the specific details of each probe mapping for a given probe set. Associated Gene information is also reported, which is derived from the transcript mapping process. The mapping process is a two step procedure out-lined in the <a href='/htdocs/info/docs/microarray_probe_set_mapping.html'>Microarray Probe Set Mapping<\a> document.
+1 probe2Transcript Microarray Probe Sets Ensembl annotates microarray probe sets on the genome sequences if manufacturers disclosed individual probe set sequences for a particular micro array. The Ensembl 'ContigView' displays probes that match to the current assembly. If not displayed by default, microarray probe set tracks are available from the 'Features' menu in the yellow menu bar of the 'Detailed View' panel. Pointing at a particular probe in a probe set track displays a pop-up window which links to the probe set details on the FeatureView page. Here a karyotype image is annotated with probe locations accompanied by a table listing the specific details of each probe mapping for a given probe set. Associated Gene information is also reported, which is derived from the transcript mapping process. The mapping process is a two step procedure out-lined in the <a href='/htdocs/info/docs/microarray_probe_set_mapping.html'>Microarray Probe Set Mapping<\a> document.
1 Arma_ab_initio_RepeatMask Repeats (Armadillo) Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using ab initio repeat profiles specific to Dasypus novemcinctus.
1 Arma_sup_RepeatMask Repeats (Armadillo +) Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using a supplemental repeat database specific to Dasypus novemcinctus.
1 BACends BAC ends Bacterial Artificial Chromosome (end sequences) of library clones that were used in the sequencing project are aligned to the genome using <a rel="external" href="http://www.sanger.ac.uk/Software/analysis/SSAHA2/">SSAHA2</a>.
-1 BlastmiRNA miRNA(miRBase) Positions of miRNAs along the genome are shown. A BLASTN of genomic sequence regions against <a rel="external" href="http://microrna.sanger.ac.uk">miRBase</a> sequences is performed, and hits are clustered and filtered by E value. Aligned genomic sequence is then checked for possible secondary structure using RNAFold. If evidence is found that the genomic sequence could form a stable hairpin structure the locus is used to create a miRNA gene model. The resulting BLAST hit is used as supporting evidence for the miRNA gene. See <a href="/info/docs/genebuild/ncrna.html" class="cp-external">article</a>.
+1 BlastmiRNA miRNA(miRBase) Positions of miRNAs along the genome are shown. A BLASTN of genomic sequence regions against <a rel="external" href="http://microrna.sanger.ac.uk">miRBase</a> sequences is performed, and hits are clustered and filtered by E value. Aligned genomic sequence is then checked for possible secondary structure using RNAFold. If evidence is found that the genomic sequence could form a stable hairpin structure the locus is used to create a miRNA gene model. The resulting BLAST hit is used as supporting evidence for the miRNA gene. See <a href="/info/docs/genebuild/ncrna.html" class="cp-external">article</a>.
1 CDM cDNAs (Tetraodon) Tetraodon cDNAs were prepared from 7 adult tissues by Genoscope, and aligned using BLAST and EST2GENOME <a rel="externa" href="http://www.ncbi.nlm.nih.gov/pubmed/9283765?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum">(R. Mott, Comput Appl Biosci. 1997 13:477-8)</a>.
1 cDNA_update cDNA (updated) The latest set of cDNAs for this species from EMBL-nucleotides and NCBI RefSeq were aligned to the current genome using <a rel="external" href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a>.
-1 CpG CpG islands CpG islands are regions of nucleic acid sequence containing a high number of adjacent cytosine guanine pairs (along one strand). Usually unmethylated, they are associated with promoters and regulatory regions. They are determined from the genomic sequence using a program written by G. Miklem, similar to <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/newcpgreport.html">newcpgreport</a> in the EMBOSS package.
+1 CpG CpG islands CpG islands are regions of nucleic acid sequence containing a high number of adjacent cytosine guanine pairs (along one strand). Usually unmethylated, they are associated with promoters and regulatory regions. They are determined from the genomic sequence using a program written by G. Miklem, similar to <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/newcpgreport.html">newcpgreport</a> in the EMBOSS package.
1 Dust Low- complexity (Dust) 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.
1 EG3_F Conserved regions (Takifugu and Tetraodon) Evolutionary conserved regions ("Ecores") are inferred from alignments of the Takifugu and Tetraodon genomes by <a rel="external" href="http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html">Exofish, H. Roest Crollius et al.,</a> and grouped into contiguous, consistent sets ("Ecotigs")
1 EG3_H Conserved regions (Human and Tetraodon) Evolutionary conserved regions ("Ecores") are inferred from alignments of the Human and Tetraodon genomes by <a rel="external" href="http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html">Exofish, H. Roest Crollius et al.,</a> and grouped into contiguous, consistent sets ("Ecotigs")
@@ -35,7 +35,7 @@
1 FANTOM_GSC_PET_raw Fantom GSC raw These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 FANTOM_GIS_PET Fantom GIS ditags These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 FANTOM_GIS_PET_raw FANTOM GIS ditags raw These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
-1 Fgenesh Gene prediction (FGENESH) Ab initio prediction of protein coding genes, based on the genomic sequence alone <a rel="external" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10779491">AA Salamov et al., Genome Res. 2000 4:516-22</a>.
+1 Fgenesh Gene prediction (FGENESH) Ab initio prediction of protein coding genes, based on the genomic sequence alone <a rel="external" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10779491">AA Salamov et al., Genome Res. 2000 4:516-22</a>.
1 FirstEF First exon finder First Exon Finder (<a rel="external"href="http://www.nature.com/ng/journal/v29/n4/full/ng780.html">First EF</a>) predicts positions of the first exons of transcripts, both coding and non-coding, using the sequence to identify features such as CpG islands and promoter regions.
1 GID Gene prediction (geneid) Ab initio prediction of protein coding genes by <a rel="external" href="http://www1.imim.es/software/geneid/">Geneid</a>, with parameters customised for accuracy in Tetraodon sequences.
1 GSC Gene prediction (Genscan) Ab initio prediction of protein coding genes by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc">Genscan</a>, with parameters customised for accuracy in Tetraodon sequences
@@ -56,7 +56,7 @@
1 PercentageRepeat Repeats (percent) Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.)
1 Pfam Protein domains (Pfam) Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D138?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Bateman&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT">Pfam </a>database.
1 Prints Protein domains (Prints) 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=&HITS=10&hits=10&RESULTFORMAT=1&author1=Attwood&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT">PRINTS </a>database.
-1 PrositePatterns Protein domains (ProSite patterns) Hits to the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D134">PROSITE patterns</a> database; protein family/domain models based on regular expressions.
+1 PrositePatterns Protein domains (ProSite patterns) Hits to the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D134">PROSITE patterns</a> database; protein family/domain models based on regular expressions.
1 PrositeProfiles Protein domains (ProSite profiles) Hits to the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D134">PROSITE profiles</a> database; protein family/domain models based on weight matrices.
1 Pseudogene Pseudogenes Pseudogenes are identified from the Ensembl <a href="/info/docs/genebuild/genome_annotation.html" class="cp-external">gene set</a> (predicted by <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>/Exonerate) on the basis of frameshifted introns (introns of less than 10bp) and intron repeat content (introns of more than 80% repeat). See <a href="/info/docs/genebuild/genome_annotation.html#Other" class="cp-external">article</a> for more.
1 RFAM ncRNA (RFAM) <a href="/info/docs/genebuild/ncrna.html" class="cp-external">Positions</a> of ncRNAs (non-coding RNAs) from the <a rel="external" href="http://www.sanger.ac.uk/Software/Rfam/">Rfam </a> database are shown.
@@ -68,7 +68,7 @@
1 Smart Protein domains (SMART) Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D257?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=letunic&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=1/1/2006&tdate=12/31/2006&resourcetype=HWCIT">SMART </a>database.
1 Stick_ab_initio_RepeatMask Repeats (Stickleback) Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> using ab initio repeat profiles specific to Gasterosteus aculeatus.
1 Stick_sup_RepeatMask Repeats (Stickleback +) Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> using a supplemental repeat database specific to Gasterosteus aculeatus.
-1 Superfamily Protein domains (Superfamily) Protein domains and motifs in the <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457CXWM-3D&_user=776054&_coverDate=11%2F02%2F2001&_rdoc=17&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236899%232001%23996869995%23286382%23FLA%23display%23Volume)&_cdi=6899&_sort=d&_docanchor=&_ct=17&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=a921e84cd71c59f75644aa28f3224b58"> SUPERFAMILY</a> database.
+1 Superfamily Protein domains (Superfamily) Protein domains and motifs in the <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457CXWM-3D&_user=776054&_coverDate=11%2F02%2F2001&_rdoc=17&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236899%232001%23996869995%23286382%23FLA%23display%23Volume)&_cdi=6899&_sort=d&_docanchor=&_ct=17&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=a921e84cd71c59f75644aa28f3224b58"> SUPERFAMILY</a> database.
1 Supp_RepeatMask Repeats + Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> using a supplemental repeat database specific to the species.
1 TRF Repeats (tandem) <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/27/2/573?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Benson&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=1/1/1999&tdate=12/31/1999&resourcetype=HWCIT">Tandem Repeats Finder</a> locates adjacent copies of a pattern of nucleotides.
1 Tenrec_ab_initio_RepeatMask Repeats (Tenrec) Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> using ab initio repeat profiles specific to Echinops telfairi.
@@ -143,22 +143,22 @@
1 flyreg Binding site (TF) Drosophila melanogaster transcription factor binding sites from the DNase I footprint database <a rel="external" href="http://umber.sbs.man.ac.uk/bergman/data/Bergman2004/v2.0/Footprint.html">FlyReg 2.0</a> <a rel="external" href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/8/1747">Bergman, C. M. et al.</a>
1 guineapig_cdna Transcripts (Guineapig) Guineapig cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 guineapig_est ESTs (Guineapig) Guineapig 'Expressed Sequence Tags' (ESTs) from the <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> database are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
-1 havana Genes (Vega) Manually annotated transcripts (determined on a case-by-case basis) from the Vega <a rel="external" href="http://www.sanger.ac.uk/HGP/havana/havana.shtml">Havana</a> project.
+1 havana Genes (Vega) Manually annotated transcripts (determined on a case-by-case basis) from the Vega <a rel="external" href="http://www.sanger.ac.uk/HGP/havana/havana.shtml">Havana</a> project.
1 human_cdna Trancripts (Human) Human cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 human_ensembl_proteins Proteins (Human, Ensembl) Selected Ensembl-predicted human peptide sequences aligned to the genome using the whole genome alignment to gene (WGA2Gene) projection method or <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 human_est ESTs (Human) Homo sapiens 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 human_one2one_mus_orth Orthologues (human to mouse) Human ensembl transcripts that are <a href="/info/docs/compara/homology_method.html" class="cp-external">one-to-one orthologues</a> with mouse are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
-1 human_protein Proteins (Human, UniProt) Human proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
-1 human_refseq Proteins (Human, RefSeq) Human proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
+1 human_protein Proteins (Human, UniProt) Human proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
+1 human_refseq Proteins (Human, RefSeq) Human proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
1 insertion_site Insertion Site (Fly) Feature imported from<a rel="external" href="http://www.flybase.org">FlyBase</a> gff files.
-1 jgi_v1 Genes (C. intestinalis, JGI v1) Alignments to Ciona intestinalis gene models predicted by <a rel="external" href="http://www.jgi.doe.gov/genome-projects/">JGI</a> on <a rel="external" href="http://www.sciencemag.org/cgi/content/full/298/5601/2157">assembly version 1.0</a>.
-1 knownGeneDensity Genes (density) Known gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/">gene_density_calc.pl</a>.
+1 jgi_v1 Genes (C. intestinalis, JGI v1) Alignments to Ciona intestinalis gene models predicted by <a rel="external" href="http://www.jgi.doe.gov/genome-projects/">JGI</a> on <a rel="external" href="http://www.sciencemag.org/cgi/content/full/298/5601/2157">assembly version 1.0</a>.
+1 knownGeneDensity Genes (density) Known gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/">gene_density_calc.pl</a>.
1 kyotograil_2004 Genes (Kyotograil, 2004) C. intestinalis gene models from the <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">KYOTOGRAIL set, version 2004,</a> aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 kyotograil_2005 Genes (Kyotograil, 2005) C. intestinalis gene models from the <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">KYOTOGRAIL set, version 2005,</a> aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 macaque_cdna Transcripts (Macaque) Macaque cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 macaque_est ESTs (Macaque) Macaque 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 macaque_protein Proteins (Macaque, UniProt) Macaque proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
-1 macaque_refseq Proteins (Macaque, RefSeq) Macaque proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
+1 macaque_refseq Proteins (Macaque, RefSeq) Macaque proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
1 mammal_protein Proteins (Mammal, UniProt) Mammalian proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
1 mapping Genes (Yeast) Yeast genes are aligned against genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Note: these are no longer used.
1 mature_peptide Mature Peptide (Fly) Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>.
@@ -191,14 +191,14 @@
1 rat_cdna Transcripts (Rat, RefSeq/EMBL) Rattus norvegicus cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 rat_est ESTs (Rat) Rattus norvegicus 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 regulatory_region Regulatory Region (Fly) Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>.
-1 rescue_fragment Rescue Fragment Feature (Fly) imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>.
+1 rescue_fragment Rescue Fragment Feature (Fly) imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>.
1 rodent_protein Proteins (Rodent, RefSeq/TrEMBL) Rodent Proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://uniprot.org">UniProtKB/TrEMBL</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
1 savignyi_est ESTs (C. savignyi) Ciona savignyi 'Expressed Sequence Tags' (ESTs) were aligned to corrected cDNA sequences from the <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">Kyoto-EST-set</a> using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 scaffold Scaffold (Fly) Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>.
1 scanprosite Protein domains (PROSITE) 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.
1 sheep_bac_ends BAC ends (Sheep) Sheep Bacterial Artificial Chromosome (end sequences) are aligned to the genome sequence using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 signal_peptide Signal Peptide (Fly) Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>.
-1 singapore_est Genes (Singapore) Expressed Sequence Tag (EST)-based gene prediction provided by B. Kumarasamy and E. Stupka.
+1 singapore_est Genes (Singapore) Expressed Sequence Tag (EST)-based gene prediction provided by B. Kumarasamy and E. Stupka.
1 singapore_protein Genes (Singapore) Protein-based gene-prediction
1 snpDensity SNP Density Density of Single Nucleotide Polymorphisms (SNPs) calculated by variation_density.pl (see scripts at the <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/">Sanger Centre CVS</a> repository).
1 stickleback_EST ESTs (Stickleback) Gasterosteus aculeatus 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
@@ -238,5 +238,4 @@
1 tetraodon_est ESTs (Tetraodon) Tetraodon 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 fugu_protein Proteins (Takifugu) Takifugu proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
1 tetraodon_protein Proteins (Tetraodon) Tetraodon proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>.
-
-1 genedensity Genes (density) Known gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/">gene_density_calc.pl</a>.
+1 genedensity Genes (density) Known gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/">gene_density_calc.pl</a>.
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