Dear All
I am performing BLAST. The database is a collection of short protein sequences (~40 aa in length, short but not short very much). The query file contains short protein sequences as well (~40 aa). I found BLASTp E-value cutoff of 1e-5 works badly. What's your suggestions on doing this BLAST? Thanks a lot!
What do you mean by it works badly... too much sequence are retrieved ? Proteins are not really similar ? ... ?
Your e-value depends of the size of your query (m) and the size of your database (n).
See here: http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html
So, you can try by cheating on your database size (you can define with a parameter), or use the bit-score instead of the e-value. You can also decrease your cutoff.
I invite you to consult also this document: http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf.
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"Performing BLAST" is a very bad descriptor. What is your goal doing this? Are you looking for similar sequences? Proteins with a specific domain? Proteins which has not been observed before?
And what do you mean by "short, but not short very much"?