[Bioperl-l] Accession Nuber to Genbank Record (Isolation Source)

Brian Osborne bosborne11 at verizon.net
Fri Mar 5 15:43:33 EST 2010


Shalabh,

I see. I think you could use EUtils then. Take a look at these:

http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service

I'm not an expert on these, and I do not know if one can ask for just a tag value ("isolation_source"). Getting a tag value from the downloaded Genbank entry is not difficult though, that Feature-Annotation HOWTO shows you how.

Brian O.


On Mar 5, 2010, at 3:29 PM, shalabh sharma wrote:

> HI Brian,
>           Thanks for your quick reply.
> I was reading the document and it think it talks about parsing a GenBank
> record. What i exactly want is to submit a batch of accession numbers and
> get "isolation_source" directly without downloading all the Genbank files.
> I am still reading the document may be i missed something.
> 
> Thanks a lot
> shalabh
> 
> 
> On Fri, Mar 5, 2010 at 3:13 PM, Brian Osborne <bosborne11 at verizon.net>wrote:
> 
>> Shalabh,
>> 
>> You can start by reading about how Bioperl processes Genbank files and
>> their annotations:
>> 
>> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>> 
>> 
>> 
>> Brian O.
>> 
>> On Mar 5, 2010, at 3:06 PM, shalabh sharma wrote:
>> 
>>> Hi All,
>>>       I have a set of accession numbers. Is it possible to get
>>> "isolation_source" from the GenBank records for all the Accession
>> numbers.
>>> 
>>> I would really appreciate if anyone can help me out.
>>> 
>>> Thanks
>>> Shalabh
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
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