[Bioperl-l] Bio::SearchIO::hmmer

Thomas Sharpton thomas.sharpton at gmail.com
Wed Sep 1 17:29:26 EDT 2010


Hi Shalabh,

We forked the SearchIO parser for hmmer3 and hmmer2. You'll want to  
use the HMMER3 version, as found here:

http://github.com/bioperl/bioperl-hmmer3

Hope this helps,
T

On Sep 1, 2010, at 1:56 PM, shalabh sharma wrote:

> Hi ,
>     I am trying to parse hmmsearch report (from HMMER3). I am using  
> the
> script mentioned here:
> http://search.cpan.org/~birney/bioperl-1.2.3/Bio/SearchIO/hmmer.pm
>
> I am not getting anything but this "amoA_10genes_align.fasta.2   
> [M=247] for
> HMM" as the output, i am not even getting any error.
> I am attaching the hmmsearch report (just a test report) which i  
> tried to
> test against the parser.
>
> I would really appreciate if anyone can help me out.
>
> Thanks
> Shalabh Sharma
> <test_amao.txt>_______________________________________________
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