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 rg] >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 output_pssm If you have the O'Reilly BLAST book, it's described starting on page 258. HTH, Joey > >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 do >it for you? > >I am sure you can find something on google somewhere if you keep looking >:) > > > >> >>Thanks in advance. >> >>Rajesh >>_______________________________________________ >>ssml-general mailing list >>ssml-general at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/ssml-general >> > >_______________________________________________ >ssml-general mailing list >ssml-general at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/ssml-general