[Bioperl-l] extract protein sequence

Jason Stajich jason at bioperl.org
Sun Dec 12 15:10:21 EST 2010


But CJ wants the subseq
Something like this would get the sub-feature.
for my $feat ( $seq->get_SeqFeatures ) {
  if( $feat->primary_tag eq 'mat_peptide' ) {
    my $subfeatseq = $seq->trunc($feat->start, $feat->end);
    my ($prod) = $feat->get_tag_values('product');
    $subfeatseq->display_id($prod);
    $out->write_seq($subfeatseq);
  }
}

See also staring around slide 23:
 
http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf


Jordi Durban wrote:
> Try using:
> use Bio::DB::GenBank;
> use Bio::AnnotatableI;
>
> And something like:
> my $prot_obj = $gb->get_Seq_by_acc( $prot_id );
> $out->write_seq( $prot_obj );
>
> It could be useful.
> Hope this helps.
> 2010/12/12 C.J.<biocjh at gmail.com>
>
>> Hi Chris,
>>
>> There is a example. I want to extract the VP4 sequence from the file
>> listing blow:
>> Could you tell me how to do this with bio-perl?
>> Thanks!
>>
>> ***********************
>> LOCUS       ACF74968                  69 aa            linear   VRL
>> 02-AUG-2008
>> DEFINITION  polyprotein [Human enterovirus 71].
>> ACCESSION   ACF74968
>> VERSION     ACF74968.1  GI:194485377
>> DBSOURCE    accession EU862482.1
>> KEYWORDS    .
>> SOURCE      Human enterovirus 71
>>   ORGANISM  Human enterovirus 71
>>             Viruses; ssRNA positive-strand viruses, no DNA stage;
>>             Picornavirales; Picornaviridae; Enterovirus; Human enterovirus
>> A.
>> REFERENCE   1  (residues 1 to 69)
>>   AUTHORS   Li,Y., Qian,Y., Zhu,R., Deng,J., Zhao,L., Wang,F., Liu,L.,
>> Sun,Y.,
>>             Chen,D., Zhang,Y., Jia,L., Ding,Y., Dong,H. and Zhang,S.
>>   TITLE     Sequence analysis of VP4 of Enterovirus 71 isolated in Beijing
>>             between 2007 and 2008
>>   JOURNAL   Unpublished
>> REFERENCE   2  (residues 1 to 69)
>>   AUTHORS   Li,Y., Qian,Y., Zhu,R., Deng,J., Zhao,L., Wang,F., Liu,L.,
>> Sun,Y.,
>>             Chen,D., Zhang,Y., Jia,L., Ding,Y., Dong,H. and Zhang,S.
>>   TITLE     Direct Submission
>>   JOURNAL   Submitted (27-JUN-2008) Laboratory of Virology, Capital
>> Institute
>>             of Pediatrics, Number 2, Yabao Road, Chaoyang District, Beijing
>>             City 100020, The People's Republic of China
>> COMMENT     Method: conceptual translation.
>> FEATURES             Location/Qualifiers
>>      source          1..69
>>                      /organism="Human enterovirus 71"
>>                      /strain="BJ97"
>>                      /host="Homo sapiens"
>>                      /db_xref="taxon:39054"
>>                      /country="China: Beijing"
>>                      /collection_date="May-2008"
>>      Protein         1..>69
>>                      /product="polyprotein"
>>      mat_peptide     1..69
>>                      /product="VP4"
>>      Region          2..69
>>                      /region_name="Pico_P1A"
>>                      /note="Picornavirus coat protein (VP4); pfam02226"
>>                      /db_xref="CDD:145404"
>>      CDS             1..69
>>                      /coded_by="EU862482.1:1..>207"
>> ORIGIN
>>         1 mgsqvstqrs gshensnsat egstinytti nyykdsyaat agkqslkqdp dkfanpvkdi
>>        61 ftemaaplk
>> //
>> *******************
>>
>>
>> 2010/12/7 Chris Fields<cjfields at illinois.edu>:
>>> On Dec 6, 2010, at 11:29 PM, C.J. wrote:
>>>
>>>> Dear all,
>>>>
>>>> I have download many polyprotein sequences from Genbank.
>>>> As the polyprotein sequence contains several mature peptides.
>>>> I want to extract my target mature peptide from these sequences.
>>>> Anyone would be kind to tell me any model in Bioperl can do this?
>>>> Thanks.
>>>>
>>>> --
>>>> Regards!
>>>> C.J.
>>> You'll need to provide some example accessions to look at.  My guess is,
>> if the mature peptide is described as a feature, then yes.
>>> chris
>>>
>>>
>>>
>>
>>
>> --
>> Regards!
>> C.J.
>>
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>>
>
>
>

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



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