[Bioperl-l] can't retrive certain sequences from remote db

[Brian Osborne]

Alice,

AJ322540 is in the database, as in:

~/bioperl-live>perl -e 'use Bio::DB::GenBank;$db = new Bio::DB::GenBank;
$seq =
$db->get_Seq_by_acc("AJ322540");print $seq->seq;'
GCGGCCGCGTCGGCTGGGGCAGGGGTCGGGGGCGGCGGCAGGGGACGGGAGGGGGCCGCGGGGGACCCGACAGGGG
ACG
AGGAGGCCGCAGTAGAACCGGCTGGGAACGGGGTTGGTCGGGGGAGTCGGGACAGGGGTCGGGGCCGCCGCGGCGG
AGG
GGGAGGTGCCCGGGCGGTGCCAGGCCGCACCTCTGGAAAACGTTCCACAGGAAGCTCTGGTCCGGCAGCGCCGCGC
CTG
AGCAGGCCCAGGGCCGGCCCCAGGGCCGGGGCGGTAAGAGTAGGCGGCCATGGGCCAAGGCACGCGGCTGGGCTGA
GGC
CCTGCATCGACAAGAGACCTTTCAGGCCGACTCCGCTTCCGCCTCTGCCGGGGGCAGGGCCTGTCATTATCACCAC
TTC
GGGGGCGCAGGAAATGCGTGGTTTCCGGGATGGTAACGGGGTCCCGCGCAGCCAATTCCTTTGGAAGTTTAGTTGC
CAG
CAACGCCTTTGGCTCCTTGGGGGGAGGGCGGGGTTTTGGGCCCCTGGAGGAAACCCAAAATTTTTGGCGACAGCCC
GCC
TGCCCGCTGTGCCCAAAAAAGGCTTTGGGAAAAAATTGCTCGGGCCCTTGAACTTTGGTAGAGGAAGGATTGTGCC
CCC
CTCTTTTTGGCTTTTTAGTTTTTAATAAAAAAACTTGGGGGGGATGTGTTTTATGTAACACTGCGTGAAATTTGGT
GGG
GGGCGGGGTGTCTATCACTAGATTTCTTCCTTTTTTGTGGGCGAGTAGGAATGAATTTTTTTTTCCCACTTTTTTT
CTC
ACCTCGTGGAAGTTGTATCCCCCCTCTCCCTAAATACATACATATTATTGTAGGGGGGGTGTTAGGTTCACAATTA
CGG
GTGGGTGGTGGGATGTTCTTTCCCTCGGATAAATATCCTAGGTTTCCCCTTCTTTTTTTCT

Perhaps you did "use Bio::DB::GenPept"?


Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Alice Lu
Sent: Tuesday, February 11, 2003 11:38 AM
To: Bioperl list
Subject: [Bioperl-l] can't retrive certain sequences from remote db

Hi everyone,

Why is that I can't retrieve certain sequences from remote database? For the
following example, I have tried:

 $seq=$gb->get_Seq_by_Acc("AJ322540");
or
 $seq=$gb->get_Seq_by_gi("15866774");

Both failed. In the meantime, it works for some other Accession Numbers. it
looks like some sequences just aren't in the database even though they have
accession number and GI number. The reason? I don't know.

Any suggestions will be appreciated.

Alice


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