19 months ago by
Vienna - BOKU
what should be my blastp parameters, to get only significant match ?
This question groups together with "what is the cure of cancer".
Functional annotation is a pain in the a**, you have to deal with it. There are no "optimal" parameters, and many results in the databases are either wrong or "unknown", "uncharacterized", "undefined".
From your command I can see that you are limiting the hits to 1 and the high-scoring pairs to 1 (hsp). Why? Are you working in a non-model organism I assume (like I do) so you did a gene prediction because there was none. However, you could allow for more hsps than 1 because many times you have more than 1 hsp per sequence. There is one script (this: find-best-hit.py ) which allows you to find the best combination of HSPs in a blast run from an xml output file. Give it a try!