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?