Question: How to create PSSM matrix
0
gravatar for sepehr.salsabili
15 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 • 717 views
ADD COMMENTlink modified 15 months ago by fishgolden450 • written 15 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 15 months ago • written 15 months ago by genomax91k

"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 13 months ago • written 13 months ago by fishgolden450
0
gravatar for fishgolden
15 months ago by
fishgolden450
fishgolden450 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 15 months ago by fishgolden450
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1513 users visited in the last hour