Blastx_Nhits and MinIdentity

[ac91]

Hi,

I´m running blastx but I don´t known how to get only results for 100 best hits per query and a minimum of 50% of identity. What are the options that allows me to do that?

thanks!

[jonfoox]

Hi ac91,

To limit your search to 100 best hits per query, use -max_target_seqs 100.
Note that this is different from -max_hsps, which can be used to limit the number of High Scoring Pairs (HSPs) for any given query/match.

When you say 50% identity, do you mean with respect to the query sequence? If so, you can use -qcov_hsp_perc 50.

Please note that that this is taken from the latest version of BLAST+ (2.6.0). If you are using an older version, these flags may be different (and I think -qcov_hsp_perc was only recently introduced).

In general, you can use blastx -help to get a detailed description of every flag at your disposal.

Happy BLASTing!

[ac91]

Thanks for the reply!

I´m using -max_target_seqs 100 but I have more than 100 hits per query.
I believe that max_target_seqs doesn't specify the maximum number of hits per query, but the maximum number of target sequences per query.

[jonfoox]

My guess is that your query is being matched to 100 unique hits. But for every hit, there are multiple HSPs being reported. So in total >100 matches are reported.

If you want to limit the output to just the top HSP between any given query/hit, try -max_hsps 1 (again I think the syntax for this flag changed in more recent versions of BLAST+; it used to be -max_hsps_per_subject).