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Commit 91a49392 authored by Steve Trevanion's avatar Steve Trevanion
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and more tweaks

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misc-scripts/analysis_description/analysis.descriptions
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8 GadflyX FlyBase proteins aligned by WU-BlastX GadflyX 1
9 Superfamily 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 domain 1 {'type'=>'domain'}
10 caenorhabditis_mrna Caenorhabditis ESTs aligned to the genome using BLAT (excluding C.elegans) caenorhabditis cDNA 1 {'type'=>'rna'}
11 est_exonerate 'Expressed Sequence Tags' (ESTs) are mapped onto the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. EST 1 {'label_key' => '[text_label] [display_label]','type' => 'est'}
11 est_exonerate 'Expressed Sequence Tags' (ESTs) are mapped onto the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. EST 1 {'type' => 'est'}
12 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. Low complexity (Dust) 1
13 FANTOM_GSC_PET 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>. Fantom GSC ditags 1
14 mouse_cdna Murine 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://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;resourcetype=HWCIT">GeneWise</a>. Mouse RefSeq/EMBL cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
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103 transposable_element Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. TE 1
104 fugu_cDNA Takifugu cDNAs from <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/Genbank/">Genbank</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Takifugu cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
105 ensembl_segment Immunoglubulin (Ig) and T-cell receptor (TcR) genes are imported from the <a rel="external" href="http://imgt.cines.fr">IMGT database</a> and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. See <a href="/info/docs/genebuild/ig_tcr.html" class="cp-external">article</a>. Ig/T-cell receptor gene 1 {'caption' => 'Ensembl/Havana gene','name' => 'Merged Ensembl and Havana Genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'},'key' => 'ensembl'}
106 chimp_cdna Pan troglodytes 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>. Chimpanzee cDNA 1 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
106 chimp_cdna Pan troglodytes 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>. Chimpanzee cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
107 qtl Quantitative Trait Loci (QTL) features. QTL 1
108 Tmhmm 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
109 rat_cdna 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>. Rat RefSeq/EMBL cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
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117 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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;resourcetype=HWCIT">GeneWise</a>. Macaque RefSeq prot. 1
118 macaque_est 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>. Macaque EST 1 {'type'=>'est'}
119 macaque_protein 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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;resourcetype=HWCIT">GeneWise</a>. Macaque UniProt prot. 1
120 ncRNA Non-coding RNA (ncRNA) is predicted using sequences from <a href="http://www.sanger.ac.uk/Software/Rfam/index.shtml">RFAM</a> and <a href="http://microrna.sanger.ac.uk/sequences/index.shtml">miRBase</a>. See <a href="/info/docs/genebuild/ncrna.html" class="cp-external">article</a>. ncRNA gene 1 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'}}
120 ncRNA Non-coding RNA (ncRNA) is predicted using sequences from <a href="http://www.sanger.ac.uk/Software/Rfam/index.shtml">RFAM</a> and <a href="http://microrna.sanger.ac.uk/sequences/index.shtml">miRBase</a>. See <a href="/info/docs/genebuild/ncrna.html" class="cp-external">article</a>. ncRNA gene 1 {'colour_key' => 'rna_[status]','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'}}
121 xlaevis_EST Xenopus laevis '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>. X.laevis EST 1 {'type'=>'est'}
122 snpDensity 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). SNP Density 1
123 Medaka_TranscriptCoalescer Medaka genes, predicted using Medaka ESTs as input for the gene-predicting module TranscriptCoalescer. EST-based gene 1 {'label_key' => '[text_label] [display_label]','label' => '[text_label] [display_label]'}
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220 platypus_est Platypus 'Expressed Sequence Tags' (ESTs) from <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>. Platypus EST 1 {'type'=>'est'}
221 Signalp 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
222 ensembl_IG_gene Immunoglobulin (Ig) and T-cell receptor (TcR) genes were imported from the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D593?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Lefranc&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;resourcetype=HWCIT">IMGT</a> database using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Ig/T-cell receptor gene 1 {'colour_key' => '[biotype]','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'}}
223 horse_cdna Horse 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>. Horse cDNA 1 {'gene' => {'do_not_display' => 1},'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
223 horse_cdna Horse 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>. Horse cDNA 1 {'gene' => {'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
224 horse_protein Horse protein sequences from <a rel="external" href="http://uniprot.org">UniProtKB</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;resourcetype=HWCIT">GeneWise</a>. Horse prot. 1
225 Est2genome_human Alignment of human ESTs (expressed sequence tags) to the genome using the program <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/est2genome.html">Est2genome</a>. ESTs are from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> Human EST (EST2genome) 1 {'type'=>'est'}
226 Est2genome_mouse Alignment of mouse ESTs (expressed sequence tags) to the genome using the program <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/est2genome.html">Est2genome</a>. ESTs are from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> Mouse EST (EST2genome) 1 {'type'=>'est'}
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