[Bioperl-l] a stupid question

Barry Moore bmoore at genetics.utah.edu
Wed Sep 28 00:23:21 EDT 2005

Depends on what your Gene IDs are.  If they are IDs to contigs or
bacterial genomes or something like that and you want fasta sequence
then just past a comma separated list of them into Entrez and Bob's your
uncle.  If your sequences are for cDNA, EST then use UCSC's Table
Browser to pull the equivalent sequences off the genome for you.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Sean Davis
Sent: Tuesday, September 27, 2005 4:37 AM
To: xuying; Bioperl
Subject: Re: [Bioperl-l] a stupid question

On 9/27/05 3:20 AM, "xuying" <xuying at sibs.ac.cn> wrote:

> Dear All:
>       I have a file containing wanted genes' GeneIDs. How can I map
> GeneID to its Fasta sequence (genomic sequence of the gene)? Although
There is
> position and contig information in the gene2accession file... Is there
> simple way? Thanks!

You truly want the genomic sequence for a given gene, or do you want the
spliced transcript?  The spliced transcripts are called refseqs in NCBI
parlance and there may be zero to many refseqs for each Gene ID.  There
a number of ways to get the refseq sequences.  You can use NCBI ftp to
the mRNA for them, or you can use Ensembl or UCSC to get the genomic
versions of them (the spliced genomic sequence).  If you truly want the
"locus" associated with a given Gene ID, I don't know where that
is stored in an easily-retrievable, standardized place, but Stefan may
able to tell you how to get it from the ASN1 files from NCBI.  (Stefan?)


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