In a genome database (nucleotide sequence) located in my computer, I would like to identify a given conserved domain, e.g., a given PSSM or a given Pfam.
For this purpose, I looked at PSI-BLAST and DELTA-BLAST, but they are protein-protein search tools, while I need searching a nucleotide database. Similarly, http://pfam.xfam.org/ allows searching protein-protein.
Is there any tool suitable for me to be used locally on my computer?
Dear Giovanni,
Programmes for making-using your own databases ususally paid ones. Our genetists use several for alignments, VectorNTI and Clustal are simple ones. PEAKS is both for large protein and nucleotide self-selected databases.
Thanks Jonathan. I think that RPS-BLAST should be fine. I will try it.
Elena, thanks for your suggestions. Those tools should be very interesting, but freeware is better for me :)
Thank you.
We also do not have a tradition to use paid software, and as there are good old versions in some places on line, freeware is possible sometimes :) Din't work only for PEAKS, we lost it in Russia, as it is not only impossible for key-treatment but even stubborn to sit in only one computer
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