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<DIV><FONT face=Arial>Hi Bronwen,</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>I tried Squid package just now. It works fine. Thank
you very much for the information.</FONT></DIV>
<DIV><FONT face=Arial>Have a nice weekend!</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>Sincerely,</FONT></DIV>
<DIV><FONT face=Arial>Jinfeng</FONT></DIV>
<DIV style="FONT: 10pt Tahoma">
<DIV><BR></DIV>
<DIV style="BACKGROUND: #f5f5f5">
<DIV style="font-color: black"><B>From:</B> <A title=ba1@sanger.ac.uk
href="mailto:ba1@sanger.ac.uk">Bronwen Aken</A> </DIV>
<DIV><B>Sent:</B> Friday, November 26, 2010 5:37 PM</DIV>
<DIV><B>To:</B> <A title=jfchen@genetics.ac.cn
href="mailto:jfchen@genetics.ac.cn">Chen Jinfeng</A> </DIV>
<DIV><B>Cc:</B> <A title=dev@ensembl.org
href="mailto:dev@ensembl.org">dev@ensembl.org</A> </DIV>
<DIV><B>Subject:</B> Re: [ensembl-dev] program 'translate'?</DIV></DIV></DIV>
<DIV><BR></DIV>Hi Jinfeng Chen,
<DIV><BR></DIV>
<DIV>I think this comes from Sean Eddy's Squid package, which you can download
here:</DIV>
<DIV><A
href="ftp://selab.janelia.org/pub/software/squid/">ftp://selab.janelia.org/pub/software/squid/</A></DIV>
<DIV><BR></DIV>
<DIV>Cheers,</DIV>
<DIV>Bronwen</DIV>
<DIV><BR></DIV>
<DIV><BR>
<DIV>
<DIV>On 26 Nov 2010, at 02:52, Chen Jinfeng wrote:</DIV><BR
class=Apple-interchange-newline>
<BLOCKQUOTE type="cite">
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<DIV><FONT face=宋体 size=2>Hi All,</FONT></DIV>
<DIV><FONT face=宋体 size=2></FONT> </DIV>
<DIV><FONT face=宋体 size=2>Does any one know a program 'translate' with an
option -m? It was used in Bio::EnsEMBL::Analysis::Tools::TranslateTools.pm.
Runing with -m means translating DNA with Met. I have no idea where this
program from. Maybe you have familiar with this program or gramene genebuilder
pipeline. Tell me somethings. Thanks.</FONT></DIV>
<DIV><FONT face=宋体 size=2></FONT> </DIV>
<DIV><FONT face=宋体 size=2>Sincerely,</FONT></DIV>
<DIV><FONT face=宋体 size=2>Jinfeng Chen</FONT></DIV>
<DIV><FONT face=宋体 size=2></FONT> </DIV>
<DIV><FONT face=宋体 size=2></FONT> </DIV>
<DIV><FONT face=宋体 size=2> my
$command;<BR> if (
$met){<BR> $command = "translate -m
$file |";<BR> }<BR>
else{<BR> $command = "translate
$file |";<BR> }<BR> open ( ORF, $command )
|| die( "Error running translate" );<BR>
############################################################<BR>
# out put is of the form:<BR> #>
gi|20070124|ref|NM_000918.2|.44 length 62, nt
2236..2051<BR>
#AHDRRRSPGLREGEGPGLCRAPGLAATSSSSRHGGHPDRIRKSPFTQKCKSHDQSWRHCRRY<BR>
#> gi|20070124|ref|NM_000918.2|.45 length 34, nt
2047..1946<BR>
#VTMSSPAPSLPHGGQASPRRPGQGGTNTLMSKNV<BR> #>
gi|20070124|ref|NM_000918.2|.46 length 34, nt
1942..1841<BR>
#KSHRRNFQKEEKPPAGGRQRDSEHGSKHSGQTHV<BR></FONT></DIV></DIV>_______________________________________________<BR>Dev
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