<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>

CC BY-SA 4.0
2018-11-12T12:20:46.627Z
2018-11-17T12:24:53.343Z
2018-11-17T12:24:53.343Z
kInG_-_SaLeH   
<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>

CC BY-SA 4.0
2018-11-09T08:14:41.910Z
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?
llrs
CC BY-SA 4.0
2018-11-09T10:18:07.167Z
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.
kInG_-_SaLeH   
CC BY-SA 4.0
2018-11-09T10:24:31.530Z
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?
llrs
CC BY-SA 4.0
2018-11-09T10:34:51.027Z
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)
kInG_-_SaLeH   
CC BY-SA 4.0
2018-11-09T10:39:21.513Z
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?
llrs
CC BY-SA 4.0
2018-11-10T10:17:10.287Z
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?
kInG_-_SaLeH   
CC BY-SA 4.0
2018-11-11T12:32:31.687Z
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)
llrs
CC BY-SA 4.0
2018-11-12T07:55:53.093Z
@Llopis Thanks, do you know how to automatically download alignments for each protein sequence ?
kInG_-_SaLeH   
CC BY-SA 4.0
2018-11-12T07:57:12.637Z
Download from where? BLAST perhaps? In what format, and in what language ?
llrs
CC BY-SA 4.0
2018-11-12T08:18:23.330Z
From NCBI , PSI-BLAST, in xml fomat, in python
kInG_-_SaLeH   
CC BY-SA 4.0
2018-11-12T08:31:31.213Z
This would require a major re[edit] of the question. Could you please update the question to keep the question and answer related?
llrs
<python><psi-blast><pssm>
How to get PSSM of protein by protein sequence with python?
# 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?  

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## 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)).


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