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<DIV><SPAN class=390451318-26022006><FONT face=Arial color=#0000ff size=2>Use
the NCBI eutils. Submit the GenBank accession # to get the GenBank record
in XML. The XML record will contain an entry for the
organism.</FONT></SPAN></DIV><SPAN class=390451318-26022006>
<DIV><BR><FONT face=Arial><FONT color=#0000ff><FONT size=2>Here's a script I
have to do this<SPAN class=390451318-26022006>. First input is the
database, nucleotide in your case, search term is the accession #. No
options causes the results to be sent back in ASN.1 format. I forget the
option to make it xml. I think its rettype=XML or something like
that.</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=Arial><FONT color=#0000ff><FONT size=2><SPAN
class=390451318-26022006></SPAN></FONT></FONT></FONT> </DIV>
<DIV><FONT face=Arial><FONT color=#0000ff><FONT size=2><SPAN
class=390451318-26022006>You can even put your input in a text file and redirect
the file as input to the script...</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=Arial><FONT color=#0000ff><FONT size=2><SPAN
class=390451318-26022006></SPAN></FONT></FONT></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><SPAN class=390451318-26022006><FONT face=Arial color=#0000ff
size=2>---BEGIN: efetch.pl---</FONT></SPAN></DIV>
<DIV><FONT face=Arial color=#0000ff size=2>#!/usr/bin/perl -w</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>use LWP::Simple;</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>my $utils = "</FONT><A
href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils"><FONT face=Arial
size=2>http://eutils.ncbi.nlm.nih.gov/entrez/eutils</FONT></A><FONT face=Arial
color=#0000ff size=2>";</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>print "Database: ";<BR>$db =
<STDIN>;<BR>chomp $db;</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>print "Search Term: ";<BR>$term =
<STDIN>;<BR>chomp $term;</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>print "Options: ";<BR>$options =
<STDIN>;<BR>chomp $options;</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>my $esearch =
"$utils/esearch.fcgi?db=$db&term=$term&usehistory=y&tool=efetch";<BR>print
"$esearch\n";<BR>my $esearch_result = get($esearch);</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>if ($esearch_result =~
m/<Id>(\d+)<\/Id>/) {<BR>
$id = $1;<BR>}<BR>if ($esearch_result =~
m/<QueryKey>(\d+)<\/QueryKey>/)
{<BR> $key = $1;<BR>}<BR>if
($esearch_result =~ m/<WebEnv>(.*)<\/WebEnv>/)
{<BR> $webenv = $1;<BR>}</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>if (defined($id))
{<BR> print "ID: $id\nKey:
$key\nWebEnv: $webenv\n\n";</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial><FONT color=#0000ff><FONT
size=2> $esearch =
"$utils/efetch.fcgi?db=$db&id=$id&tool=efetch";<BR>
print "$esearch\n";<BR> my
$esummary_result = get($esearch);<BR>
print "$esummary_result\n";<BR>} else
{<BR> print
"$esearch_result\n";<BR>}<BR><SPAN class=390451318-26022006>---END:
efetch.ph---</SPAN></FONT></FONT></FONT></SPAN></DIV>
<DIV><SPAN class=390451318-26022006><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<BLOCKQUOTE style="MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma size=2>-----Original Message-----<BR><B>From:</B>
bio_bulletin_board-bounces+golharam=umdnj.edu@bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu@bioinformatics.org]
<B>On Behalf Of </B>Samantha Fox<BR><B>Sent:</B> Sunday, February 26, 2006
12:58 PM<BR><B>To:</B> The general forum at
Bioinformatics.Org<BR><B>Subject:</B> [BiO BB] mapping genbank accession to
Organism name<BR><BR></FONT></DIV>Hi all,<BR>This should be really easy, but
somehow I am cannot figure it out. I BLASTed my sequences with the
non-redundant nt sequence from NCBI.<BR>The hits are something like
gb|AC167666.4, emb|BX640434.1, emb|BX640418.1 ...<BR><BR>Can someone suggest
me a way to get the organism name from these genbank accessions ?<BR><BR>hope
someone has done this already :) ..<BR>~S<BR></BLOCKQUOTE></BODY></HTML>