[ssml] Multiple Alignment to PSSM

Joseph Bedell jbedell at oriongenomics.com
Fri Apr 29 14:15:35 EDT 2005

Hi Rajesh,

Joseph A Bedell, Ph.D.         office: 314-615-6979 
Director, Bioinformatics         fax:    314-615-6975 
Orion Genomics                   cell:   314-518-1343
4041 Forest Park Ave
St. Louis, MO 63108
>-----Original Message-----
>From: ssml-general-bounces+jbedell=oriongenomics.com at bioinformatics.org
>[mailto:ssml-general-bounces+jbedell=oriongenomics.com at bioinformatics.o
>On Behalf Of Dan Bolser
>Sent: Friday, April 29, 2005 7:53 AM
>To: Ratna Rajesh Thangudu
>Cc: ssml-general at bioinformatics.org
>Subject: Re: [ssml] Multiple Alignment to PSSM
>On Fri, 29 Apr 2005, Ratna Rajesh Thangudu wrote:
>>Dear All,
>>I have a set of multiple alignments which I want to convert into PSSM
>>profiles (searchable byr RPSblast). Could anyone please tell how to
>>achieve this?

[Joseph Bedell] 
You should be able to do this within NCBI BLAST using the blastpgp with
the -B  and -C options. For example:

blastpgp -i query -j 5 -d nr  -B multiple_alignment -C output_pssm

The multiple_alignment file must be based on the Clustal format but
without the header and footer. The file should have a row for each
sequence and can be broken into blocks separated by one or more blank
lines. The query file (specified by -i) must be included in the
alignment and all rows must be padded with dashes '---' to make them
equal lengths. Your PSSM, which can be used in an RPSblast, will be in

If you have the O'Reilly BLAST book, it's described starting on page


>I remember some tools to convert between HMMER / SAM / PSSM, and I know
>HMMER will make a model from a multiple alignment, so you could then
>convert your HMMER model to a PSSM. Right now I can't find the page of
>these tools. Will psiblast (or related tools in the ncbi toolkit) not
>it for you?
>I am sure you can find something on google somewhere if you keep
>>Thanks in advance.
>>ssml-general mailing list
>>ssml-general at bioinformatics.org
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