Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2017-07-02T21:04:35.520Z
Answers.LastActivityDate: 2018-07-31T08:20:59.287Z
Answers.LastEditDate: 2018-07-31T08:20:59.287Z
Answers.UserDisplayName: Joe Healey
Answers.Body: <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>
  
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Answers.LastActivityDate: 2018-07-31T15:17:48.247Z
Answers.LastEditDate: 2018-07-31T15:17:48.247Z
Answers.UserDisplayName: Matt Bashton
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-31T05:30:55.153Z
Answers.LastActivityDate: 2018-07-31T08:57:10.200Z
Answers.LastEditDate: 2018-07-31T08:57:10.200Z
Answers.UserDisplayName: Sidra Younas
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-30T14:15:32.887Z
Comments.Text: Which error did it give you the NCBI PSI-BLAST? Could you paste here the image with the options used? What have you tried to overcome this problem?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-30T14:25:28.360Z
Comments.Text: The error was: Message ID#9 Error: PSSM processing error: Incomplete PSSM with Parameters provided on input: missing score matrix
Comments.UserDisplayName: Sara
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-30T14:34:45.167Z
Comments.Text: So it seems that you need to provide the PSSM in certain format and CAPS didn't manage to create it in the expected format. Could you post the PSSM here (or in an accessible way) ? Now that I look in the help I couldn't find any reference to a specific format (just that it should be from their own output ...)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-30T14:51:02.370Z
Comments.Text: I do not exactly know how to post PSSM file here. Could you please guide me how to load a file here?
Comments.UserDisplayName: Sara
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-30T14:58:10.543Z
Comments.Text: You can't but you can copy paste the content or add a link to dropbox or a similar server
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-30T16:09:44.453Z
Comments.Text: @Llopis it should be fine posted here as code.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-30T16:10:16.723Z
Comments.Text: @Sara see [formatting tools](https://bioinformatics.stackexchange.com/help/formatting) for help on formatting your posts. For things like this, you want to use code (`{}`) which uses a fixed-width font.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-02T06:50:03.750Z
Comments.Text: I think you could use standalone blast, one example here https://www.biostars.org/p/15482/
Comments.UserDisplayName: friveroll
Tags: <blast><phylogenetics><phylogeny>
Title: A tool or webserver for building PSSM matrix
ThreadText: # A tool or webserver for building PSSM matrix
  
  (Asked by: username_0 on 2017-06-30)
  
  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](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on). I used [CHAPS](http://fasta.bioch.virginia.edu/fasta_www2/chaps.cgi) 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 } , 
  
  ```
  
  **Tags:** blast, phylogenetics, phylogeny
  
  > **Comments:**
  > **username_1**: Which error did it give you the NCBI PSI-BLAST? Could you paste here the image with the options used? What have you tried to overcome this problem?  
  > **username_0**: The error was: Message ID#9 Error: PSSM processing error: Incomplete PSSM with Parameters provided on input: missing score matrix  
  > **username_1**: So it seems that you need to provide the PSSM in certain format and CAPS didn't manage to create it in the expected format. Could you post the PSSM here (or in an accessible way) ? Now that I look in the help I couldn't find any reference to a specific format (just that it should be from their own output ...)  
  > **username_0**: I do not exactly know how to post PSSM file here. Could you please guide me how to load a file here?  
  > **username_1**: You can't but you can copy paste the content or add a link to dropbox or a similar server  
  > **username_2**: @Llopis it should be fine posted here as code.  
  > **username_2**: @username_0 see [formatting tools](https://bioinformatics.stackexchange.com/help/formatting) for help on formatting your posts. For things like this, you want to use code (`{}`) which uses a fixed-width font.  
  > **username_3**: I think you could use standalone blast, one example here https://www.biostars.org/p/15482/  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_4 on 2017-07-02. Score: 2
  
  If you take a look at my answer in this [BioStars post](https://www.biostars.org/p/259190/#259265), you can generate a PSSM using `AlignIO` in Biopython:
  
  
  ---
  
  ### Answer by username_5 on 2018-07-31. Score: 1
  
  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](https://www.ebi.ac.uk/Tools/hmmer/search/jackhmmer) 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.
  
  
  ---
  
  ### Answer by username_6 on 2018-07-31. Score: 1
  
  You can use biopython's code for generation of PSSM.
  Here is the [link](http://biopython.org/DIST/docs/api/Bio.motifs.matrix-pysrc.html) for the source code which can help you.
  
  
  ---
  
  