How to decrease computing time of reciprocal BLAST
2
0
Entering edit mode
6.3 years ago
biolab ★ 1.3k

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!

orthologous blast Reciprocal Best Hits • 1.9k views
ADD COMMENT
0
Entering edit mode

What is the command that you have tried?

ADD REPLY
0
Entering edit mode

Hi IsmaiM, 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.

blastp -query qfile -db dbfile -evalue 1e-5 -max_target_seqs 1 -outfmt 6 > result 2>log
ADD REPLY
2
Entering edit mode
3.6 years ago
Buffo ★ 1.9k

What about DIAMOND? I think it is a very good alternative to blastp.

ADD COMMENT
1
Entering edit mode
6.3 years ago
IsmailM ▴ 110

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
ADD COMMENT
0
Entering edit mode

Hi IsmaiM, thank you for your suggestions.

ADD REPLY

Login before adding your answer.

Traffic: 2798 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6