I would like on my local machine or remotely if it is possible too, launch a psiblast from a sequence. Then, like on the website of ncbi, select my own sequences from the result file. And launch another iteration from these sequences.
When I launch psiblast on local I obtain a pairwise alignment in xml or other format. How can I select my sequences to go to run another iteration? If I select sequences, I need to make a MSA so, I destroy the blast result if evalue if very high. I would like to do exactly the same choice of psiblast but in a script (which launch blast localy or remotely)
for instance :
blastpgp -i mysequence -j 1 -o mysequence.blast
--> I create a file just with the sequences that I want to keep (not only significative sequence), -> mynewsequenceTo2d_iteration
blastpgp -i mynewsequenceTo2d_iteration -j 1 -o 2diteration.blast
Is it possible? I did not find any way to do it... I make a multiple alignment between each iteration but Psiblast in ncbi do not that...
I take every way to do it, even with Biopython or CGI