Answers.Body: <p>We solve our problem and create gitHub repository (<a href="https://github.com/MsAlEhR/bio-protein-recog" rel="nofollow noreferrer">bio-protein</a>).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-12T12:20:46.627Z
Answers.LastActivityDate: 2018-11-17T12:24:53.343Z
Answers.LastEditDate: 2018-11-17T12:24:53.343Z
Answers.UserDisplayName: kInG_-_SaLeH   
Body: <p>I didn't find way that convert protein sequences in  FASTA to PSSM by python,
  and how to write program in python to find PSSM for our data set ?
  Maybe better to question how to find PSSM from NCBI alignments ?</p>
  
  <p>Thank you  </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-09T08:14:41.910Z
Comments.Text: Welcome to the site. Where did you search? Did you look up to biopython? What is your data set? A collection of fasta sequences or alignments?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-09T10:18:07.167Z
Comments.Text: Thank you for your answer , yes i check biopython , but there is no method or class that get protein sequences in fasta and return pssm  . for example from NCBI site , for each sequences.
Comments.UserDisplayName: kInG_-_SaLeH   
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-09T10:24:31.530Z
Comments.Text: Ok, so you want to retrieve from the NCBI site, download the protein sequences and then create a pssm? That is different from what you posted. Please [edit] the question to include this details. Would you be fine with a solution that worked with a local blast program?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-09T10:34:51.027Z
Comments.Text: I think better to use psi-blast from NCBI to find my alignments for each sequence  i don't know easy way to  get aligments and pass them to function to get PSSM (i dont know it is necessary to find pssm)
Comments.UserDisplayName: kInG_-_SaLeH   
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-09T10:39:21.513Z
Comments.Text: Sorry I don't understand your last comment. What are you trying to do/get? To get a PSSM you need an alignment of sequences. So you need several sequences and then align them (that's what psi-blast does). But you seem to ask about retrieving the PSSM matrix from a psi-blast search. Have you tried something else like hmmer?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-10T10:17:10.287Z
Comments.Text: Sorry , i am too beginner . Can you give me  a solution to get PSSM for each of my protein sequence with use psi blast NCBI ? I can calculate PSSM localy on my computer but how to get aligmnets?
Comments.UserDisplayName: kInG_-_SaLeH   
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-11T12:32:31.687Z
Comments.Text: Sorry it is not easy to answer your question. The alignments must be done downloading all the sequences of interest and aligning them via t-coffee or similar tools. Then you can calculate the PSSM matrix (not the other way round)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-12T07:55:53.093Z
Comments.Text: @Llopis Thanks, do you know how to automatically download alignments for each protein sequence ?
Comments.UserDisplayName: kInG_-_SaLeH   
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-12T07:57:12.637Z
Comments.Text: Download from where? BLAST perhaps? In what format, and in what language ?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-12T08:18:23.330Z
Comments.Text: From NCBI , PSI-BLAST, in xml fomat, in python
Comments.UserDisplayName: kInG_-_SaLeH   
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-12T08:31:31.213Z
Comments.Text: This would require a major re[edit] of the question. Could you please update the question to keep the question and answer related?
Comments.UserDisplayName: llrs
Tags: <python><psi-blast><pssm>
Title: How to get PSSM of protein by protein sequence with python?
ThreadText: # How to get PSSM of protein by protein sequence with python?
  
  (Asked by: username_0 on 2018-11-09)
  
  I didn't find way that convert protein sequences in FASTA to PSSM by python,
  and how to write program in python to find PSSM for our data set ?
  Maybe better to question how to find PSSM from NCBI alignments ?
  
  Thank you
  
  **Tags:** python, psi-blast, pssm
  
  > **Comments:**
  > **username_1**: Welcome to the site. Where did you search? Did you look up to biopython? What is your data set? A collection of fasta sequences or alignments?  
  > **username_0**: Thank you for your answer , yes i check biopython , but there is no method or class that get protein sequences in fasta and return pssm  . for example from NCBI site , for each sequences.  
  > **username_1**: Ok, so you want to retrieve from the NCBI site, download the protein sequences and then create a pssm? That is different from what you posted. Please [edit] the question to include this details. Would you be fine with a solution that worked with a local blast program?  
  > **username_0**: I think better to use psi-blast from NCBI to find my alignments for each sequence  i don't know easy way to  get aligments and pass them to function to get PSSM (i dont know it is necessary to find pssm)  
  > **username_1**: Sorry I don't understand your last comment. What are you trying to do/get? To get a PSSM you need an alignment of sequences. So you need several sequences and then align them (that's what psi-blast does). But you seem to ask about retrieving the PSSM matrix from a psi-blast search. Have you tried something else like hmmer?  
  > **username_0**: Sorry , i am too beginner . Can you give me  a solution to get PSSM for each of my protein sequence with use psi blast NCBI ? I can calculate PSSM localy on my computer but how to get aligmnets?  
  > **username_1**: Sorry it is not easy to answer your question. The alignments must be done downloading all the sequences of interest and aligning them via t-coffee or similar tools. Then you can calculate the PSSM matrix (not the other way round)  
  > **username_0**: @Llopis Thanks, do you know how to automatically download alignments for each protein sequence ?  
  > **username_1**: Download from where? BLAST perhaps? In what format, and in what language ?  
  > **username_0**: From NCBI , PSI-BLAST, in xml fomat, in python  
  > **username_1**: This would require a major re[edit] of the question. Could you please update the question to keep the question and answer related?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-11-12. Score: 1
  
  We solve our problem and create gitHub repository ([bio-protein](https://github.com/MsAlEhR/bio-protein-recog)).
  
  
  ---
  
  