Question: How to create PSSM matrix
0
gravatar for sepehr.salsabili
12 months ago by
sepehr.salsabili0 wrote:

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 :

downloaded format

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

blast psiblast pssm • 625 views
ADD COMMENTlink modified 12 months ago by fishgolden420 • written 12 months ago by sepehr.salsabili0

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

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax87k

"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.

ADD REPLYlink modified 11 months ago • written 11 months ago by fishgolden420
0
gravatar for fishgolden
12 months ago by
fishgolden420
fishgolden420 wrote:

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.

ADD COMMENTlink written 12 months ago by fishgolden420
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