[Bioperl-l] Question on extracting Molecular Weight fields fromUniProt records

[Chris Fields]

Information for the SQ line (length, MW, crc64) is not parsed.  On  
output everything is recalculated from scratch, with the MW being  
recalculated using SeqStats (as indicated by Marc).  I would consider  
this a feature, for if you change/modify the sequence record you would  
have to rerun all those calculations anyway.

chris

On May 19, 2008, at 10:35 AM, Marc Logghe wrote:

> Hi Anand,
> I don't believe that field is extracted. But you can calculate it  
> using
> Bio::Tools::SeqStats.
>
> my $seq_stats  =  Bio::Tools::SeqStats->new(-seq => $seq_object);
> my $weight = $seq_stats->get_mol_wt;
>
>
> HTH,
> Marc
>
> Marc Logghe
> Senior Bioinformatician
> Ablynx nv
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Anand Venkatraman
>> Sent: Saturday, May 17, 2008 12:52 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Question on extracting Molecular Weight fields
>> fromUniProt records
>>
>> Hi everybody,
>>
>> I would like to know if there is a way in which one can extract the
> value
>> from "Molecular Weight" field of a UniProt Record (for example that
> value
>> is "140080 Da" for http://www.pir.uniprot.org/cgi-
>> bin/upEntry?id=MSH6_YEAST )
>>
>> I am able to use Bio::DB::SwissProt to get the length & seq
>> $seq_length = $seq_object->length()
>> $sequence_as_a_string = $seq_object->seq();
>>
>> Is there a similar method to extract the Molecular Weight field?
>>
>> Thanks in advance,
>>
>> Anand
>>
>>
>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign