[Bioperl-l] UniGene

[iluminati at earthlink.net]

Sean,

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.

Todd

Sean Davis wrote:

> Todd,
>
> 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 
> directory:
>
> ftp://ftp.ncbi.nih.gov/gene/DATA/
>
> 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?
>
> Sean
>
> 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
>
>
>> Sean:
>>
>> 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:
>>
>>> Badr,
>>>
>>> The simplest way is to go to the ftp site for unigene:
>>>
>>> ftp://ftp.ncbi.nih.gov/repository/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.
>>> Sean
>>>
>>> ----- 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
>>>>
>>>> Badr
>>>>
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>>
>
>
>