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  • Blastx_Nhits and MinIdentity

    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!

  • #2
    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!

    Comment


    • #3
      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.

      Comment


      • #4
        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).

        Comment

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