how did I miss these earlier?

misc-scripts/analysis_description/analysis.descriptions

@@ -81,9 +81,9 @@
 78	drosophila_cdna_all	Drosophila melanogaster cDNA sequences from <a rel="external" href="http://www.fruitfly.org">BDGP</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.	Fly cDNA	1	 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
 79	GID	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.	Geneid prediction	1	
 80	slimswissprotP	Swissprot proteins aligned by WU-BlastP	slimswissprotP	1	{'type'=>'alignment'}
-81	ensembl_havana_gene	Gene containing both Ensembl genebuild transcripts and <a rel="external" href="http://vega.sanger.ac.uk/index.html">Havana</a> manual curation, see <a href="/info/docs/genebuild/genome_annotation.html" class="cp-external">article</a>.	Ensembl/Havana merge 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'}
+81	ensembl_havana_gene	Gene containing both Ensembl genebuild transcripts and <a rel="external" href="http://vega.sanger.ac.uk/index.html">Havana</a> manual curation, see <a href="/info/docs/genebuild/genome_annotation.html" class="cp-external">article</a>.	Ensembl/Havana merge gene	1	 {'colour_key' => '[biotype]_[status]','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'}'
 82	ncoils	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	
-83	havana	Manually annotated transcripts (determined on a case-by-case basis) from the <a rel="external" href="http://www.sanger.ac.uk/HGP/havana/havana.shtml">Havana</a> project.	Vega 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'}
+83	havana	Manually annotated transcripts (determined on a case-by-case basis) from the <a rel="external" href="http://www.sanger.ac.uk/HGP/havana/havana.shtml">Havana</a> project.	Vega gene	1	 {'colour_key' => '[biotype]_[status]','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'}'
 84	Pfam	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 domain	1	{'type'=>'domain'}
 85	PercentGC	Percentage of G/C bases in the sequence.	GC content	1	
 86	knownGeneDensity	Known gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/">gene_density_calc.pl</a>.	Genes (density)	1	
@@ -105,7 +105,7 @@
 102	Marker	Markers, or sequence tagged sites (STS), from <a rel="external" href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists">UniSTS</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/full/7/5/541">Electronic PCR (e-PCR)</a>.	Marker	1	
 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'}
+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	 {'colour_key' => '[biotype]_[status]','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	 {'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	
@@ -249,7 +249,7 @@
 246	Operon	Multi-gene feature imported from <a rel="external" href="http://www.wormbase.org">Wormbase</a> annotation.	Operon	1	
 247	platypus_cdna	Platypus 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>.	Platypus cDNA	1	 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
 248	RepeatMasker_TIGR	Interspersed repeats identified by RepeatMasker (http://www.repeatmasker.org/)	RepeatMask	1	
-249	ensembl_havana_transcript	Transcript where the Ensembl genebuild transcript and the <a rel="external" href="http://vega.sanger.ac.uk/index.html">Vega</a> manual annotation have the same sequence, for every base pair.  See <a href="/info/docs/genebuild/genome_annotation.html" class="cp-external">article</a>.	Ensembl/Havana merge transcript	1	
+249	ensembl_havana_transcript	Transcript where the Ensembl genebuild transcript and the <a rel="external" href="http://vega.sanger.ac.uk/index.html">Vega</a> manual annotation have the same sequence, for every base pair.  See <a href="/info/docs/genebuild/genome_annotation.html" class="cp-external">article</a>.	Ensembl/Havana merge transcript	1	{'colour_key' => '[biotype]_[status]','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'}	
 250	Uniprot_mammal	Mammalian proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted mammalian peptides to UniProtKB proteins.	mammal UniProt prot.	1	
 251	fosmid	Vancouver fosmids mapped to the C.elegans genome (available through GeneService)	fosmid	1	
 252	CYT	Cytokine gene, structure manually curated by Genoscope,	Cytokine gene	1	 {'label' => '[text_label] [display_label]'}