Benjamin Buchfink
Benjamin Buchfink
Sorry for the late reply. Yes, the BLAST-like table is missing in this format. I need to add this when I find the time.
You can try to use diamond blastx to align any DNA sequence, if it's not protein coding you will not find anything.
The diamond v2 paper has a benchmark of these sensitivity modes: https://www.nature.com/articles/s41592-021-01101-x
The columns are explained here: https://github.com/bbuchfink/diamond/wiki/1.-Tutorial >how to parameter the tool in term of e-value, qcov_hsp_perc etc All options are explained in the Wiki. > final question how I could...
There are other tools that can do that, but diamond works only on proteins.
> otherwise I still can apply blastx using swissprot by applyinf this command: Yes of course you can use the blastx mode of diamond.
I will run some tests and see if I can reproduce the issue.
No this is not supported.
qcovs and qcovhsp are the same most of the time. When there are multiple HSPs in the same subject, qcovs is the combined coverage while qcovhsp is the coverage of...
Sure, you can use any database with the same command line.