How to decrease computing time of reciprocal BLAST
Hi, everyone,
I am using Reciprocal Best Hits (RBH) method to group orthologous proteins from diverse species. I have 50 eukaryotic species at hand, so should do 49x50 BLASTs. I found it needs much time, even setting evalue = 1e-5 and getting top hit.
Is there any way to improve my work? I learned some parallel technology is powerful, but don't know how to start. Any of your suggestions will be appreciated. THANK YOU very much!
2 answers
Blastp takes an argument (-num_threads) where you can specify the number of threads to use. Run the following
blastp -num_threads 8 -query qfile -db dbfile -evalue 1e-5 -max_target_seqs 1 -outfmt 6 >result 2>log
See the following for more information:
blastp -h
Or for even more information:
blastp -help
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What is the command that you have tried?
Hi IsmailM, The following is my command. I am sure BLASTP is time-consuming. I am trying UBLAST (a program in USEARCH), which is better. However, handling 50 species is still time-consuming. Any of your suggestions will be appreciated.