[Bioperl-l] Collecting genomic DNA sequences using Entrez IDs

Barry Moore barry.moore at genetics.utah.edu
Fri Nov 30 17:03:23 EST 2007


Paul,

One other alternative is to use the UCSC table browser (http:// 
genome.ucsc.edu/cgi-bin/hgTables?command=start).  Select your  
organism, upload your ID list.  Select you output options.  You can  
download the coordinates or the fasta directly.  You have options for  
including or excluding various parts of the gene, and upstream/ 
downstream sequences.  This is similar the solution that Malcom  
suggested except the Ensembl option can be run repeatedly as perl  
code as he pointed out.  UCSC allows you to do remote connections to  
their MySQL server so you could set up a repeated task and more  
complex queries that way with the UCSC method.

Barry

On Nov 30, 2007, at 7:12 AM, Cook, Malcolm wrote:

> How many, how often?
>
> Use ensembl biomart!
>
> First time interactively.
>
> Then if you to pipeline it, take the perl code it generates for you  
> and
> run it - of course you'll have to install the Ensembl Perl API....
>
>
> Malcolm Cook
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, Missouri
>
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>> Paul N. Hengen
>> Sent: Wednesday, November 28, 2007 7:21 PM
>> To: Bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Collecting genomic DNA sequences using Entrez  
>> IDs
>>
>>
>> Hi.
>>
>> I have a number of gene IDs from Entrez and I want to find
>> the start and end locations in the human genome. This seemed
>> simple enough, so I started working through some of the
>> examples for using the EntrezGene module at www.bioperl.org
>> Of course this did not work because the core installation
>> does not include this module. So, I think I have two choices
>> (1) install the module (how?), or (2) find an easier way to
>> get the locations in the human genome.
>> I want to use the locations to grab sequences out of the genome.
>> Can anyone offer advice on this? Thanks.
>>
>> -Paul.
>>
>> --
>> Paul N. Hengen, Ph.D.
>> Hematopoietic Stem Cell and Leukemia Research City of Hope
>> National Medical Center 1500 E. Duarte Road, Duarte, CA 91010
>> USA mailto:paulhengen at coh.org
>>
>> --
>> View this message in context:
>> http://www.nabble.com/Collecting-genomic-DNA-sequences-using-E
>> ntrez-IDs-tf4894403.html#a14017289
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>
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