How to create PSSM matrix

Question

[sepehr.salsabili]

Hi, I have an course project and I need to create a PSSM matrix. I run online psiblast for 3 iteration and get a pssm matrix but my professor gave us a specific pssm matrix type wich we should get it from a local blast run. ![needed format[1]

but I have downloaded this as a pssm :

does anybody can guide me how to get what I want from downloaded pssm or online blast? thank every body in advance,

[GenoMax]

Please use instead of the image provider you are using : How to add images to a Biostars post

[fishgolden]

"I have downloaded this as a pssm"

It's ASN.1 format. You can use it as input file of sofware/web-service in my answer.

I can't see needed format[1] yet.

[Somayeh]

Hi. How to get pssm matrix ? Thank you.

Answer 1

[fishgolden]

I can't see [needed format[1] and downloaded format.

But do you mean that you need ascii format?

You can use PSSM viewer.

https://www.ncbi.nlm.nih.gov/Class/Structure/pssm/pssm_viewer.cgi

Enter PSSM to view, Scoremat file -> Matrix View -> Download Matrix to File

or try local psi-blast with -num_iterations 1 and -out_ascii_pssm

psiblast -in_pssm <path to your checkpoint asn.1 pssm> -db <any db> -num_iterations 1 -out_ascii_pssm <output file name>

psi-blast WITHOUT "-save_pssm_after_last_round" returns INPUT pssm thus "-num_iterations 1" would return pssm you provided.