[Bioperl-l] Reading a XML sequence (UniParc) into a BioSeq object

Samuel GRANJEAUD - IR/IFR137 granjeau at tagc.univ-mrs.fr
Mon Feb 26 04:17:15 EST 2007


Hello !

I would like to fill a BioSeq object with the output from a dbfetch
request at EI on UniParc database (which replies only XML code, as I am
interested in references). If somebody could tell which BioPerl object
to use or a way or convert it in Swiss format or could tell me the way
to do it or has got a piece of code (is
http://doc.bioperl.org/bioperl-live/Bio/SeqIO/interpro.html a good
starting point), I would appreciate a lot.

Best regards,
--Samuel

<entry accession="UPI00004A0D4A">
<dbReferenceList>
    <dbReference db="EMBL" id="CAI39485" version="1" version_i="1" 
active="Y" created="04-Jan-2005" last="15-Dec-2006"/>
    <dbReference db="UniProtKB/TrEMBL" id="Q5JVT0" version="1" 
version_i="1" active="N" created="15-Feb-2005" last="06-Feb-2007"/>
    <dbReference db="ENSEMBL" id="ENSP00000352958" version_i="2" 
active="Y" created="03-Apr-2006" last="27-Nov-2006"/>
    <dbReference db="IPI" id="IPI00418471" version="4" version_i="4" 
active="N" created="07-Mar-2005" last="07-Mar-2005"/>
    <dbReference db="IPI" id="IPI00646867" version="1" version_i="1" 
active="N" created="06-Sep-2005" last="06-Oct-2006"/>
    <dbReference db="VEGA" id="OTTHUMP00000019225" version_i="1" 
active="N" created="15-Aug-2005" last="02-Dec-2005"/>
</dbReferenceList>
<sequence length="431" crc64="8913D1F04A71CCFB">
MSTRSVSSSSYRRMFGGPGTASRPSSSRSYVTTSTRTYSLGSALRPSTSRSLYASSPGGV
YATRSSAVRLRSSVPGVRLLQDSVDFSLADAINTEFKNTRTNEKVELQELNDRFANYIDK
VRFLEQQNKILLAELEQLKGQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAE
DIMRLREKLQEEMLQREEAENTLQSFRQDVDNASLARLDLERKVESLQEEIAFLKKLHEE
EIQELQAQIQEQHVQIDVDVSKPDLTAALRDVRQQYESVAAKNLQEAEEWYKSKFADLSE
AANRNNDALRQAKQESTEYRRQVQSLTCEVDALKGTNESLERQMREMEENFAVEAANYQD
TIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNFSS
LNLRGKHFISL
</sequence>
</entry>





More information about the Bioperl-l mailing list