[BiO BB] Re: Quickly retrieving cross-referenced records from NCBI

[Gaj Stan (BIGCAT)]

No problem. Well, I didn't know the trick through NCBI. So I learned a
bit out of this as well. (-; 
On the other hand, I'd like to do those 'smaller' tasks myself, so I
understand the processes behind it and know for sure that it happened in
a correct manner. But that's just a personal view on it! (-;

Oh, and just for completeness sake, I noticed that the maillist does not
support attachments, so I've uploaded the script (if you or someone else
might ever need it *cough*) to
http://ftp2.bigcat.unimaas.nl/~stan.gaj/scripts/refseq_converter_np2nm.p
l

Best wishes to you all for 2007!
 
   Stan

-----Original Message-----
From:
bio_bulletin_board-bounces+stan.gaj=bigcat.unimaas.nl at bioinformatics.org
[mailto:bio_bulletin_board-bounces+stan.gaj=bigcat.unimaas.nl at bioinforma
tics.org] On Behalf Of Dale Richardson
Sent: 21 December 2006 04:32
To: General Forum at Bioinformatics.Org
Subject: Re: [BiO BB] Re: Quickly retrieving cross-referenced records
from NCBI

Hi Stan,

Thanks for this!  I will definitely keep a hold of it.  However, I  
think there is yet another way to retrieve such cross-ref'd records:   
For example, if I input a set of XP_ accessions and want to get the  
XM_ accessions one can simply select, "Nucleotide links" from the  
pulldown menu at NCBI (where GenPept, FASTA and other such options  
are listed).

Thanks for your tips tho (and to everyone else as well)!

Hope everyone has a great holiday season.

-dale


On Dec 20, 2006, at 12:02 PM, Gaj Stan (BIGCAT) wrote:

> Dear Dale,
>
> I encountered the same question a few weeks ago, but my focus was the
> other way around: go from NM to NP. For that I've written a Perl  
> script
> that I've adjusted to fit your needs (so going for NP to NM).
>
> If I'm correct, RefSeq splits it's database in three parts: genomic,
> mRNA and protein. For this script to work, you need a) to download a
> species-specific RefSeq mRNA database (ends with .rna.gbff) for the  
> NCBI
> ftp and b) to have your own file of convertable IDs, sorted in a
> list-form..
> Note that this script will NOT detect version numbers: e.g. XP_12345.1
> needs to be converted to XP_12345 in your list before it does it's  
> job!
>
> Although the code is far from perfect, it fulfills your question
> perfectly (-;
>
> Best wishes,
>
>    Stan
>
>
> -----Original Message-----
> From:
> bio_bulletin_board-bounces 
> +stan.gaj=bigcat.unimaas.nl at bioinformatics.org
> [mailto:bio_bulletin_board-bounces 
> +stan.gaj=bigcat.unimaas.nl at bioinforma
> tics.org] On Behalf Of Eugene Bolotin
> Sent: 13 December 2006 19:30
> To: General Forum at Bioinformatics.Org
> Subject: Re: [BiO BB] Re: Quickly retrieving cross-referenced records
> from NCBI
>
> The quickest way is UCSC table browser, batch retreive. Read up on  
> that.
>
>
> On 12/12/06, Dale Richardson <dalesan at gmail.com> wrote:
>>
>> Hello All,
>>
>> Forgive me for posting, but this question is hard to condense into a
>> good google search.  I am wondering if there is a quick way to batch
>> retrieve all coding sequences (mRNA sequences) linked to a particular
>> NCBI RefSeq Protein identifier.  For example, if I have a list of 10
>> sequences with the following protein refseq IDs:
>>
>> XP_698519.1
>> XP_697978.1
>>
>> and so on..
>>
>> How can I retrieve the cross-referenced XM_ identifiers for the
>> coding sequences based on such protein accessions?  Must one write
>> some kind of script to accomplish this or is there a quicker way?
>>
>> thanks,
>>
>> dale richardson
>> university of cologne
>>
>> _______________________________________________
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>
>
>
> -- 
> Eugene Bolotin
> Ph.D. candidate
> Genetics Genomics and Bioinformatics
> University of California Riverside
> ybolo001 at student.ucr.edu
> Dr. Frances Sladek Lab
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