Question: How To Set The Parameter Of Detecting Conservation Using Psiblast Or Other Tools?
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gravatar for Ct586
6.8 years ago by
Ct586530
China
Ct586530 wrote:

HI, all

I have a protein sequence and its orthologs. I want to detect if a segment(length ranges from 7 to 100) of that protein sequence also exists in its orthologs. That is to see, I want to know if it is conserved.

I used psiblast like this

psiblast -query proseg.fa -out proseg.out -db ortholog

But as some of the segments are very short, the resulted Evalue is very high. So sometimes I could even not detect the existence of that segment in its own protein.

I tried to enlarge "-inclusion_ethresh" and "-threshold" and 'set dbsize', it did return some hits. But the result is not well. And also I am not sure if the modified parameter is meaningful. Is there a formula to compute this?

Can you give me any advice on how to set the parameter or choosing other methods to do this?

Thank You!

conservation orthologues • 1.5k views
ADD COMMENTlink modified 4.9 years ago by Biostar ♦♦ 20 • written 6.8 years ago by Ct586530

Later, I find that add the following parameter "-evalue 20000 -matrix PAM30 -comp_based_stats 0" can solve this question which is the same solution used by psiblast in NCBI web site.

ADD REPLYlink written 6.8 years ago by Ct586530

I'm a bit surprised by the PAM30 matrix. Can you post the link where you found the values?

ADD REPLYlink written 6.8 years ago by Michael Schubert6.8k

Just click http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome and choose "psiblast" and give a short sequence, likely shorter than 20 amino acids. Then run blast, in the result page, you will see after you find and click the "Edit and resubmit".

ADD REPLYlink written 6.8 years ago by Ct586530
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