[ensembl-dev] program 'translate'?
Chen Jinfeng
jfchen at genetics.ac.cn
Fri Nov 26 09:54:24 GMT 2010
Hi Bronwen,
I tried Squid package just now. It works fine. Thank you very much for the information.
Have a nice weekend!
Sincerely,
Jinfeng
From: Bronwen Aken
Sent: Friday, November 26, 2010 5:37 PM
To: Chen Jinfeng
Cc: dev at ensembl.org
Subject: Re: [ensembl-dev] program 'translate'?
Hi Jinfeng Chen,
I think this comes from Sean Eddy's Squid package, which you can download here:
ftp://selab.janelia.org/pub/software/squid/
Cheers,
Bronwen
On 26 Nov 2010, at 02:52, Chen Jinfeng wrote:
Hi All,
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.
Sincerely,
Jinfeng Chen
my $command;
if ( $met){
$command = "translate -m $file |";
}
else{
$command = "translate $file |";
}
open ( ORF, $command ) || die( "Error running translate" );
############################################################
# out put is of the form:
#> gi|20070124|ref|NM_000918.2|.44 length 62, nt 2236..2051
#AHDRRRSPGLREGEGPGLCRAPGLAATSSSSRHGGHPDRIRKSPFTQKCKSHDQSWRHCRRY
#> gi|20070124|ref|NM_000918.2|.45 length 34, nt 2047..1946
#VTMSSPAPSLPHGGQASPRRPGQGGTNTLMSKNV
#> gi|20070124|ref|NM_000918.2|.46 length 34, nt 1942..1841
#KSHRRNFQKEEKPPAGGRQRDSEHGSKHSGQTHV
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