[Bioperl-l] extract protein sequence

C.J. biocjh at gmail.com
Sun Dec 12 11:45:59 EST 2010


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  JOURNAL   Unpublished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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