[Bioperl-l] extract protein sequence

Jordi Durban jordi.durban at gmail.com
Sun Dec 12 15:02:49 EST 2010


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  JOURNAL   Unpublished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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>



-- 
Jordi


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