Question: Using NCBI database in DIAMOND BLAST
0
gravatar for glady
20 months ago by
glady240
glady240 wrote:

I want to use NCBI protein(nr) database in DIAMOND BLAST. But it is always giving some database extension format error. The commands for standalone BLAST and DIAMOND BLAST are different. And also the database format required for DIAMOND BLAST is different from the normal BLAST. Hence, I'm not able to download and use the Protein database from NCBI directly since, it is always giving some DB extension error. How should I proceed ?

blast • 2.1k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 20 months ago by glady240
1
gravatar for genomax
20 months ago by
genomax64k
United States
genomax64k wrote:

You need to recreate the nr database for DIAMOND using the fasta nr file that you can download here. Are you trying to re-use the pre-formatted nr database as is?

ADD COMMENTlink modified 20 months ago • written 20 months ago by genomax64k
0
gravatar for Sej Modha
20 months ago by
Sej Modha4.1k
Glasgow, UK
Sej Modha4.1k wrote:

I've had this issue in past and I believe that's due to the fact that sometimes sequences end up with certain special characters in the fasta file. I tend to edit those sequences (usually one or two) using sed or something and then it works for me.

ADD COMMENTlink modified 20 months ago • written 20 months ago by Sej Modha4.1k
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