[Bioperl-l] Bio::SeqIO::swiss.pm module help
Brian Osborne
bosborne11 at verizon.net
Sun Jul 5 02:50:40 UTC 2009
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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