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

Chris Fields cjfields at uiuc.edu
Mon May 19 13:07:35 EDT 2008


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






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