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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

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closed as unclear what you're asking by llrs, Bioathlete, winni2k, Kamil S Jaron, Kohl Kinning Dec 7 '18 at 18:17

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

  • $\begingroup$ 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? $\endgroup$ – llrs Nov 9 '18 at 8:14
  • $\begingroup$ 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. $\endgroup$ – kInG_-_SaLeH Nov 9 '18 at 10:18
  • $\begingroup$ 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? $\endgroup$ – llrs Nov 9 '18 at 10:24
  • $\begingroup$ 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) $\endgroup$ – kInG_-_SaLeH Nov 9 '18 at 10:34
  • $\begingroup$ 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? $\endgroup$ – llrs Nov 9 '18 at 10:39
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We solve our problem and create gitHub repository (bio-protein).

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