[Biojava-l] bioJava & swissProt parsering

[wanner.de@pg.com]

Hi,

Has anyone used bioJava to parse a swissProt record.  I've attached an example
below -- it's format looks much different from
either genbank or refseq.

thx,
Dave


ID   100K_RAT       STANDARD;      PRT;   889 AA.
AC   Q62671;
DT   01-NOV-1997 (Rel. 35, Created)
DT   01-NOV-1997 (Rel. 35, Last sequence update)
DT   16-OCT-2001 (Rel. 40, Last annotation update)
DE   100 kDa protein (ENZYME: 6.3.2.-).
OS   Rattus norvegicus (Rat).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
OX   NCBI_TaxID=10116;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=WISTAR; TISSUE=Testis;
RX   MEDLINE=92253337: PubMed=1533713;
RA   Mueller D., Rehbein M., Baumeister H., Richter D.;
RT   "Molecular characterization of a novel rat protein structurally
RT   related to poly(A) binding proteins and the 70K protein of the U1
RT   small nuclear ribonucleoprotein particle (snRNP).";
RL   Nucleic Acids Res. 20:1471-1475(1992).
RN   [2]
RP   ERRATUM.
RA   Mueller D., Rehbein M., Baumeister H., Richter D.;
RL   Nucleic Acids Res. 20:2624-2624(1992).
CC   -!- FUNCTION: E3 UBIQUITIN-PROTEIN LIGASE WHICH ACCEPTS UBIQUITIN FROM
CC       AN E2 UBIQUITIN-CONJUGATING ENZYME IN THE FORM OF A THIOESTER AND
CC       THEN DIRECTLY TRANSFERS THE UBIQUITIN TO TARGETED SUBSTRATES (BY
CC       SIMILARITY). THIS PROTEIN MAY BE INVOLVED IN MATURATION AND/OR
CC       POST-TRANSCRIPTIONAL REGULATION OF MRNA.
CC   -!- TISSUE SPECIFICITY: HIGHEST LEVELS FOUND IN TESTIS. ALSO PRESENT
CC       IN LIVER, KIDNEY, LUNG AND BRAIN.
CC   -!- DEVELOPMENTAL STAGE: IN EARLY POST-NATAL LIFE, EXPRESSION IN
CC       THE TESTIS INCREASES TO REACH A MAXIMUM AROUND DAY 28.
CC   -!- MISCELLANEOUS: A CYSTEINE RESIDUE IS REQUIRED FOR
CC       UBIQUITIN-THIOLESTER FORMATION.
CC   -!- SIMILARITY: A CENTRAL REGION (AA 485-514) IS SIMILAR TO THE
CC       C-TERMINAL DOMAINS OF MAMMALIAN AND YEAST POLY (A) RNA BINDING
CC       PROTEINS (PABP).
CC   -!- SIMILARITY: CONTAINS MIXED-CHARGE DOMAINS SIMILAR TO RNA-BINDING
CC       PROTEINS.
CC   -!- SIMILARITY: CONTAINS 1 HECT-TYPE E3 UBIQUITIN-PROTEIN LIGASE
CC       DOMAIN.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL: X64411
DR   InterPro: IPR000569
DR    IPR002004
DR   Pfam: PF00632
DR    PF00658
DR   SMART: SM00119
DR    SM00517
DR   PROSITE: PS50237
KW   Ubiquitin conjugation; Ligase.
FT   DOMAIN       77     88       ASP/GLU-RICH (ACIDIC).
FT   DOMAIN      127    150       PRO-RICH.
FT   DOMAIN      420    439       ARG/GLU-RICH (MIXED CHARGE).
FT   DOMAIN      448    457       ARG/ASP-RICH (MIXED CHARGE).
FT   DOMAIN      485    514       PABP-LIKE.
FT   DOMAIN      579    590       ASP/GLU-RICH (ACIDIC).
FT   DOMAIN      786    889       HECT.
FT   DOMAIN      827    847       PRO-RICH.
FT   BINDING     858    858       UBIQUITIN (BY SIMILARITY).
SQ   SEQUENCE   889 AA;  100368 MW;  ABD7E3CD53961B78 CRC64;
     MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK AMNQQTTLDT
     PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN HPFFRRSDSM
     TFLGCIPPNP FEVPLAEAIP LADQPHLLQP NARKEDLFGR PSQGLYSSSA GSGKCLVEVT
     MDRNCLEVLP TKMSYAANLK NVMNMQNRQK KAGEDQSMLA EEADSSKPGP SAHDVAAQLK
     SSLLAEIGLT ESEGPPLTSF RPQCSFMGMV ISHDMLLGRW RLSLELFGRV FMEDVGAEPG
     SILTELGGFE VKESKFRREM EKLRNQQSRD LSLEVDRDRD LLIQQTMRQL NNHFGRRCAT
     TPMAVHRVKV TFKDEPGEGS GVARSFYTAI AQAFLSNEKL PNLDCIQNAN KGTHTSLMQR
     LRNRGERDRE REREREMRRS SGLRAGSRRD RDRDFRRQLS IDTRPFRPAS EGNPSDDPDP
     LPAHRQALGE RLYPRVQAMQ PAFASKITGM LLELSPAQLL LLLASEDSLR ARVEEAMELI
     VAHGRENGAD SILDLGLLDS SEKVQENRKR HGSSRSVVDM DLDDTDDGDD NAPLFYQPGK
     RGFYTPRPGK NTEARLNCFR NIGRILGLCL LQNELCPITL NRHVIKVLLG RKVNWHDFAF
     FDPVMYESLR QLILASQSSD ADAVFSAMDL AFAVDLCKEE GGGQVELIPN GVNIPVTPQN
     VYEYVRKYAE HRMLVVAEQP LHAMRKGLLD VLPKNSLEDL TAEDFRLLVN GCGEVNVQML
     ISFTSFNDES GENAEKLLQF KRWFWSIVER MSMTERQDLV YFWTSSPSLP ASEEGFQPMP
     SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV
//