[Bioperl-l] extract protein sequence

[Chris Fields]

+1 on this, which uses the Bio::FeatureHolder API.  See also the Feature-Annotation HOWTO:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

chris

On Dec 12, 2010, at 2:10 PM, Jason Stajich wrote:

> 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  JOURNAL   Unpublished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.
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
>> 
> 
> -- 
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
> 
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