source: orange-bioinformatics/docs/reference/obiHomoloGene.htm @ 1634:32373d957326

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Renamed addon reference documentation.

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1<html>
2
3<head>
4<title>obiHomoloGene: Translation of homologs</title>
5<link rel=stylesheet href="../style.css" type="text/css">
6<link rel=stylesheet href="style-print.css" type="text/css" media=print>
7</head>
8
9<body>
10<h1>obiHomoloGene Translation of homolog genes</h1>
11<p>obiHomoloGene is an interface to <a href="http://www.ncbi.nlm.nih.gov/homologene/">HomoloGene</a>.
12<p class=section>Functions</p>
13<dl class=attributes>
14    <dt>all_genes(taxid)</dt>
15    <dd>Return a set of all genes with known homologs for organism with <code>taxid</code></dd>
16    <dt>homologs(genename, taxid)</dt>
17    <dd>Return a list of homologs (homolog_taxid, homolog_genename) for a homolog group that <code>genename, taxid</code> belong to</dd>
18    <dt>homolog(genename, taxid, homolotaxid)</dt>
19    <dd>Return a homolog of <code>genename, taxid</code> in organism with holomotaxid or None if homolog does not exist.</dd>
20</dl>
21
22<h2>Examples</h2>
23<p>Mapping homologs from yeast to human (<a href="obiHomoloGene-yeast-to-human.py">obiHomoloGene-yeast-to-human.py</a>)</p>
24<xmp class=code>import orange
25import obiHomoloGene, obiTaxonomy, obiGene
26
27data = orange.ExampleTable("../../../../doc/datasets/brown-selected")
28
29geneinfo = obiGene.NCBIGeneInfo('4932')
30
31genes = [str(ex["gene"]) for ex in data]
32
33for gene in genes:
34    mappedgene = obiHomoloGene.homolog(geneinfo(gene).symbol, '4932', '9606')
35    print gene, mappedgene</xmp>
36<h1>InParanoid orthologs</h1>
37<p>You can also access InParanoid otrhologs database with the <code>orhologs</code> function</p>
38
39<dl class=attributes>
40    <dt>homologs(genename, taxid, ortholog_taxid=None)</dt>
41    <dd>Return all orthologs of <code>genename</code> from organism with <code>taxid</code>. If <code>ortholog_taxid</code> is given limit to orthologs from that organism only.</dd>
42    <dt>all_genes_inParanoid(taxid)</dt>
43    <dd>Return a set of all genes for organism with <code>taxid</code> in the InParanoid database</dd>
44</dl>
45 
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