[Bioperl-l] Bio::SeqIO::swiss.pm module help

[Brian Osborne]

yewcoccus,

You took a look at the Feature-Annotation HOWTO?

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


Brian O.


On Jul 4, 2009, at 10:39 PM, yewcoccus wrote:

> Hi all,
>
>      I want to parse uniprot_sprot.dat, get each of the features.  
> but I found it is hard to understand how to use the  
> Bio::SeqIO::swiss.pm module.  I will be appreciate if there is  
> anyone  who can help.
>
>
>
> ID   002R_IIV3               Reviewed;         458 AA.
> AC   Q197F8;
> DT   16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
> DT   11-JUL-2006, sequence version 1.
> DT   16-JUN-2009, entry version 10.
> DE   RecName: Full=Uncharacterized protein 002R;
> GN   ORFNames=IIV3-002R;
> OS   Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent  
> virus).
> OC   Viruses; dsDNA viruses, no RNA stage; Iridoviridae;  
> Chloriridovirus.
> OX   NCBI_TaxID=345201;
> OH   NCBI_TaxID=7163; Aedes vexans (Inland floodwater mosquito)  
> (Culex vexans).
> OH   NCBI_TaxID=42431; Culex territans.
> OH   NCBI_TaxID=332058; Culiseta annulata.
> OH   NCBI_TaxID=310513; Ochlerotatus sollicitans (eastern saltmarsh  
> mosquito).
> OH   NCBI_TaxID=329105; Ochlerotatus taeniorhynchus.
> OH   NCBI_TaxID=7183; Psorophora ferox.
> RN   [1]
> RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
> RX   PubMed=16912294; DOI=10.1128/JVI.00464-06;
> RA   Delhon G., Tulman E.R., Afonso C.L., Lu Z., Becnel J.J., Moser  
> B.A.,
> RA   Kutish G.F., Rock D.L.;
> RT   "Genome of invertebrate iridescent virus type 3 (mosquito  
> iridescent
> RT   virus).";
> RL   J. Virol. 80:8439-8449(2006).
> CC    
> -----------------------------------------------------------------------
> CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
> CC   Distributed under the Creative Commons Attribution-NoDerivs  
> License
> CC    
> -----------------------------------------------------------------------
> DR   EMBL; DQ643392; ABF82032.1; -; Genomic_DNA.
> DR   RefSeq; YP_654574.1; -.
> DR   GeneID; 4156251; -.
> PE   4: Predicted;
> FT   CHAIN         1    458       Uncharacterized protein 002R.
> FT                                /FTId=PRO_0000377938.
> SQ   SEQUENCE   458 AA;  53921 MW;  E46E5C85D7ACA139 CRC64;
>     MASNTVSAQG GSNRPVRDFS NIQDVAQFLL FDPIWNEQPG SIVPWKMNRE QALAERYPEL
>     QTSEPSEDYS GPVESLELLP LEIKLDIMQY LSWEQISWCK HPWLWTRWYK DNVVRVSAIT
>     FEDFQREYAF PEKIQEIHFT DTRAEEIKAI LETTPNVTRL VIRRIDDMNY NTHGDLGLDD
>     LEFLTHLMVE DACGFTDFWA PSLTHLTIKN LDMHPRWFGP VMDGIKSMQS TLKYLYIFET
>     YGVNKPFVQW CTDNIETFYC TNSYRYENVP RPIYVWVLFQ EDEWHGYRVE DNKFHRRYMY
>     STILHKRDTD WVENNPLKTP AQVEMYKFLL RISQLNRDGT GYESDSDPEN EHFDDESFSS
>     GEEDSSDEDD PTWAPDSDDS DWETETEEEP SVAARILEKG KLTITNLMKS LGFKPKPKKI
>     QSIDRYFCSL DSNYNSEDED FEYDSDSEDD DSDSEDDC
> //
>
> 2009-07-05
>
>
>
> yewcoccus
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