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


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

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  • $\begingroup$ 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

We solve our problem and create gitHub repository (bio-protein).


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