the best advertisement for BioMart is that almost every how do i map X to Y on Biostar must be "use BioMart"
Is there a convenient way to map Gene IDs to their locus on the human genome?
4 answers
Ensembl supports a large number of accession formats; hopefully your Gene IDs will fall into one of these formats.
In general, to get all sorts of information on a list of accessions:
- Go to Ensembl's BioMart
- Choose
Ensembl Genes 63database - Choose the data set of interest (e.g.,
Homo sapiens genes) - In the left side panel, click on
Filters - Unfold the
GENESsection on the resulting page - Check the
ID list limitbox, the origin of your gene accessions, (e.g., "Refseq Genomic ID(s)"), and either paste your accessions or upload a file - In the left side panel, click
Attributes - Choose various values you want to see for each gene you've provided (e.g., under
GENE, choosechromosome name,gene start, andgene end - Along the top nav bar, click
Results - Download results, and click the
Perlbutton for an example of how to use the API for programmatic access
Yup. Take home message: check the "related questions" box first :)
You could use Ensembl Biomart for this. Just make a text file (or copy paste) the Gene IDs to the filter list (after selecting human, under filter go to Gene and select your Gene ID type). At the attributes page you can easily select what information for each gene should be selected.
what about that gene which is from other species which not included in database?
how we find that gene map?
Please post this as a new question. Deleting...
bioDBnet is really a great web servise--> https://biodbnet-abcc.ncifcrf.gov/db/db2db.php reference:Gene Id Conversion Tool
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And what IDs are you talking about?
Entrez Gene IDs