Question: Using NCBI database in DIAMOND BLAST
0
gravatar for glady
2.4 years ago by
glady260
glady260 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 • 3.1k views
ADD COMMENTlink modified 2.0 years ago by Biostar ♦♦ 20 • written 2.4 years ago by glady260
1
gravatar for genomax
2.4 years ago by
genomax75k
United States
genomax75k 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 2.4 years ago • written 2.4 years ago by genomax75k
0
gravatar for Sej Modha
2.4 years ago by
Sej Modha4.5k
Glasgow, UK
Sej Modha4.5k 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 2.4 years ago • written 2.4 years ago by Sej Modha4.5k
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