text: user818: I have some protein sequences and I want to build a position-specific scoring matrix (PSSM) for them and then upload this PSSM to NCBI PSI-BLAST. I used CHAPS program for this pupose but uploading the output PSSM gave me an error in NCBI PSI-BLAST. Do you know any tool or webserver for getting PSSMs for a group of protein sequences which then can work in NCBI PSI-BLAST?
  This is a part of my PSSM file: 
  PssmWithParameters ::= {
  pssm {
      isProtein TRUE ,
      numRows 28 ,
      numColumns 131 ,
      byRow FALSE ,
      query
      seq {
          id {
              other {
                  accession "WP_000208753" } } ,
          inst {
              repr raw ,
              mol aa ,
              length 131 ,
              seq-data
              ncbieaa "MTTKRKPYVRPMTSTWWKKLPFYRFYMLREGTAVPAVWFSIELIFGLFALKNGPEAW
  AGFIDFLQNPVIVIINLITLAAALLHTKTWFELAPKAANIIVKDEKMGPEPIIKSLWAVTVVATIVILFVALYW" } } ,
      intermediateData {
          freqRatios {
              { 0, 10, 0 } ,
              { 564418841, 10, -10 } ,
              { 0, 10, 0 } ,
              { 11768571, 10, -9 } ,
              { 185838265, 10, -10 } ,
              { 31496547, 10, -9 } ,
              { 3872857, 10, -8 } ,
              { 291750464, 10, -10 } ,
              { 128450763, 10, -10 } ,
              { 759856221, 10, -10 } ,
              { 359173937, 10, -10 } ,
              { 179865517, 10, -9 } ,
              { 14537895, 10, -8 } ,
              { 212921456, 10, -10 } ,
              { 220554141, 10, -10 } ,
              { 368516324, 10, -10 } ,
              { 319343525, 10, -10 } ,
              { 426173953, 10, -10 } ,
              { 463659523, 10, -10 } ,
              { 817322186, 10, -10 } ,
              { 811693964, 10, -11 } ,
              { 0, 10, 0 } ,
              { 227810064, 10, -10 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 768325726, 10, -10 } ,
              { 0, 10, 0 } ,
              { 1425562, 10, -8 } ,
              { 372685285, 10, -10 } ,
              { 466727421, 10, -10 } ,
              { 185741084, 10, -10 } ,
              { 427328646, 10, -10 } ,
              { 122594965, 10, -10 } , 
  
  
  user3142: You can use biopython's code for generation of PSSM.
  Here is the link for the source code which can help you.
  
  user1769: I'm not 100% sure what you're trying to do with regards to your search in the first place, but I recommend using Sean Eddy's program Jackhammer it's similar to PSI-BLAST but uses Hammer HMM underpinnings.
  As input it can take a single sequence, a multiple sequence alignment, or an existing HMM and then allow you to search in an iterative model building way.  You can also download an HMM too at any stage in the iterative search, as well as the results / alignment. 
  
  user929: If you take a look at my answer in this BioStars post, you can generate a PSSM using AlignIO in Biopython:
  
original_text: 818: <p>I have some protein sequences and I want to build a position-specific scoring matrix (PSSM) for them and then upload this PSSM to <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE=Proteins&amp;PROGRAM=blastp&amp;RUN_PSIBLAST=on" rel="nofollow noreferrer">NCBI PSI-BLAST</a>. I used <a href="http://fasta.bioch.virginia.edu/fasta_www2/chaps.cgi" rel="nofollow noreferrer">CHAPS</a> program for this pupose but uploading the output PSSM gave me an error in NCBI PSI-BLAST. Do you know any tool or webserver for getting PSSMs for a group of protein sequences which then can work in NCBI PSI-BLAST?
  This is a part of my PSSM file: </p>
  
  <pre><code>PssmWithParameters ::= {
  pssm {
      isProtein TRUE ,
      numRows 28 ,
      numColumns 131 ,
      byRow FALSE ,
      query
      seq {
          id {
              other {
                  accession "WP_000208753" } } ,
          inst {
              repr raw ,
              mol aa ,
              length 131 ,
              seq-data
              ncbieaa "MTTKRKPYVRPMTSTWWKKLPFYRFYMLREGTAVPAVWFSIELIFGLFALKNGPEAW
  AGFIDFLQNPVIVIINLITLAAALLHTKTWFELAPKAANIIVKDEKMGPEPIIKSLWAVTVVATIVILFVALYW" } } ,
      intermediateData {
          freqRatios {
              { 0, 10, 0 } ,
              { 564418841, 10, -10 } ,
              { 0, 10, 0 } ,
              { 11768571, 10, -9 } ,
              { 185838265, 10, -10 } ,
              { 31496547, 10, -9 } ,
              { 3872857, 10, -8 } ,
              { 291750464, 10, -10 } ,
              { 128450763, 10, -10 } ,
              { 759856221, 10, -10 } ,
              { 359173937, 10, -10 } ,
              { 179865517, 10, -9 } ,
              { 14537895, 10, -8 } ,
              { 212921456, 10, -10 } ,
              { 220554141, 10, -10 } ,
              { 368516324, 10, -10 } ,
              { 319343525, 10, -10 } ,
              { 426173953, 10, -10 } ,
              { 463659523, 10, -10 } ,
              { 817322186, 10, -10 } ,
              { 811693964, 10, -11 } ,
              { 0, 10, 0 } ,
              { 227810064, 10, -10 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 0, 10, 0 } ,
              { 768325726, 10, -10 } ,
              { 0, 10, 0 } ,
              { 1425562, 10, -8 } ,
              { 372685285, 10, -10 } ,
              { 466727421, 10, -10 } ,
              { 185741084, 10, -10 } ,
              { 427328646, 10, -10 } ,
              { 122594965, 10, -10 } , 
  </code></pre>
   3142: <p>You can use biopython's code for generation of PSSM.
  Here is the <a href="http://biopython.org/DIST/docs/api/Bio.motifs.matrix-pysrc.html" rel="nofollow noreferrer">link</a> for the source code which can help you.</p>
   1769: <p>I'm not 100% sure what you're trying to do with regards to your search in the first place, but I recommend using Sean Eddy's program <a href="https://www.ebi.ac.uk/Tools/hmmer/search/jackhmmer" rel="nofollow noreferrer">Jackhammer</a> it's similar to PSI-BLAST but uses Hammer HMM underpinnings.</p>
  
  <p>As input it can take a single sequence, a multiple sequence alignment, or an existing HMM and then allow you to search in an iterative model building way.  You can also download an HMM too at any stage in the iterative search, as well as the results / alignment. </p>
   929: <p>If you take a look at my answer in this <a href="https://www.biostars.org/p/259190/#259265" rel="nofollow noreferrer">BioStars post</a>, you can generate a PSSM using <code>AlignIO</code> in Biopython:</p>
  