How to create PSSM files?

Question

[Manzoor]

I'm quite new in the field of Bioinformatics. I have around 800 protein sequences and I need to have PSSM files for each sequence. How to extract the these PSSM files?

Answer 1

[Jaykumar]

Since I also have only recently begun working in bioinformatics, my knowledge on this topic is limited. However, based on whatever I have been able to understand, here are some methods that may be helpful:

1. You could try using the POSSUM webserver, which can be found at https://possum.erc.monash.edu/.

2. Another option is to use PSI-Blast on NCBI, which is available at https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on. Alternatively, you can download the NCBI blast from NCBI and use it on the command line.

3. You could also use Biopython to parse all 800 sequences and use the Bio.Blast module there and perform psi-blast for all.

[Manzoor]

Thank you for your invaluable suggestions. I did use option 2 but the issue I'm facing is that I'm not able to download the PSSM matrix explicitly. I'm indeed missing something. I ran blast over my sequences and it gave me other sequences which were quite similar to my sequences but I need to download PSSM matrix which I'm supposed to use as an input feature in machine learning models.