Question: How to decrease computing time of reciprocal BLAST
0
gravatar for biolab
5.3 years ago by
biolab1.2k
biolab1.2k wrote:

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!

ADD COMMENTlink modified 2.6 years ago by Buffo1.8k • written 5.3 years ago by biolab1.2k

What is the command that you have tried?

ADD REPLYlink written 5.3 years ago by IsmailM110

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 REPLYlink modified 12 months ago by RamRS30k • written 5.3 years ago by biolab1.2k
2
gravatar for Buffo
2.6 years ago by
Buffo1.8k
Buffo1.8k wrote:

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

ADD COMMENTlink written 2.6 years ago by Buffo1.8k
1
gravatar for IsmailM
5.3 years ago by
IsmailM110
UK/London/University College London
IsmailM110 wrote:

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 COMMENTlink modified 12 months ago by RamRS30k • written 5.3 years ago by IsmailM110

Hi IsmaiM, thank you for your suggestions.

ADD REPLYlink written 5.3 years ago by biolab1.2k
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