[Bioperl-l] UniGene

[Sean Davis]

You can look into using eutils at NCBI, but there is not a bioperl solution 
for this as far as I know.  If you have many (1000's of genbanks), eutils 
may be slow.

If you want to make it easier to update the file, just include Net::FTP 
(available on CPAN) to grab the file for you each time you run the script.

Sean

----- Original Message ----- 
From: "badr al-daihani" <aldaihani at hotmail.co.uk>
To: <sdavis2 at mail.nih.gov>
Sent: Monday, April 18, 2005 11:42 AM
Subject: Re: [Bioperl-l] UniGene


> Dear Sean Davis
> Thank you for your reply.
> your solution is fine. but the problem, this means that I have to update 
> my file from time to time. Is any other dynamic solution which allow me to 
> connect to GenBank and fetch the UniGene using GenBank Accession
>
>
> Best regards
>
> Badr
>
>
>
>
>
>>From: "Sean Davis" <sdavis2 at mail.nih.gov>
>>To: "badr al-daihani" <aldaihani at hotmail.co.uk>, <bioperl-l at bioperl.org>
>>Subject: Re: [Bioperl-l] UniGene
>>Date: Sun, 17 Apr 2005 19:05:57 -0400
>>
>>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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