Bio::SeqIO::swiss.pm module help

[yewcoccus]

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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[Brian Osborne-2]

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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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