iluminati at earthlink.net
iluminati at earthlink.net
Mon Apr 18 16:40:21 EDT 2005
Thanks for the heads-up on Unigene vs. Gene_ID. I'll definitely take a
look-see on that. The main thing I'm looking for is a means to get
general info on what family a gene is in. I keep noticing certain kinds
of genes with similar characteristics, and all I want is a good handle
on the ballpark these genes are in. Most of the dirty work has been
done in characterizing them. I need a means for me to check what gene
is in which family, and UniGene seems like the easiest way to do so.
Sean Davis wrote:
> Probably the easiest way if you start with refseq ids (like NM_000022)
> is to map refseq to gene_id and then gene_id to unigene--are you
> starting with refseq ID's? The files to do so are located in the
> The files are pretty self-explanatory. gene2refseq and gene2unigene
> will get you what you want. They are simply tab-delimited files.
> Just make a hash keyed by refseq with value gene_id and then a hash
> with gene_id as key and a reference to an array of unigene ids as
> value (there can be more than one--or none--unigene id for each gene_id).
> What are you ultimately trying to do? There isn't much information
> associated with unigene ids anymore, and the unigene ids are only
> stable for about a month anymore. Any thought you would want to do
> your analysis using gene_id instead of unigene?
> P.S. If there isn't a reason for this NOT to go back to the bioperl
> list, it is generally OK (and VERY much encouraged) to post back to
> the list, even on these "by-the-way" questions.
> ----- Original Message ----- From: <iluminati at earthlink.net>
> To: "Sean Davis" <sdavis2 at mail.nih.gov>
> Sent: Monday, April 18, 2005 9:10 AM
> Subject: Re: [Bioperl-l] UniGene
>> I have an interesting question. I have a bunch of genes for which I
>> have RefGene ID numbers, plus a couple of tables with which I can
>> find either their KnownGene or GNFAtlas equivalents. Is there some
>> way I can get the Unigene IDs? I'd love to know if there's some easy
>> way for me to start looking at Unigene families. Thanks in advance.
>> Todd Graham
>> Sean Davis wrote:
>>> The simplest way is to go to the ftp site for unigene:
>>> Get the file for the organism you are interested that ends in
>>> .gb_cid_lid. Just choose the file for the organism of interest. For
>>> example, the first few lines of Cre.gb_cid_lid look like:
>>> AY171232 3219 -
>>> AY171231 3003 -
>>> AY171230 4370 -
>>> AY171229 2671 -
>>> AY184800 2793 -
>>> AY184799 6486 -
>>> AY184798 206 -
>>> AY184797 3607 -
>>> AY184796 2281 -
>>> AY177787 2380 -
>>> AY212923 4329 -
>>> AB091079 3370 -
>>> The first column contains genbank accessions. The second contains
>>> unigene cluster ids. So, for the first genbank AY171232, the
>>> unigene accession is Cre.3219 (You have to prepend the 2- or 3-
>>> letter organism code). You can read these into a hash that is keyed
>>> on the genbank accession with a value that is the reference to an
>>> array of unigene cluster IDs for each genbank (a genbank can be in
>>> multiple unigene clusters).
>>> Hope that helps.
>>> ----- Original Message ----- From: "badr al-daihani"
>>> <aldaihani at hotmail.co.uk>
>>> To: <bioperl-l at bioperl.org>
>>> Sent: Sunday, April 17, 2005 5:04 PM
>>> Subject: [Bioperl-l] UniGene
>>>> Hi folks
>>>> would you please tell me how to retrieve the unigene number of a
>>>> gene (UniGene)
>>>> knowing the GenBankaccession number ?
>>>> Best regards
>>>> It's fast, it's easy and it's free. Get MSN Messenger today!
>>>> Bioperl-l mailing list
>>>> Bioperl-l at portal.open-bio.org
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