What is the difference between using -max_target_seqs 1 -max_hsps 1 versus just the defaults and then filtering for top hit?

Question

[DNAngel]

Question is in the title.

Is there a difference if I use default -max_target_seqs settings in blastn (which is 5, but can return 100s of hits due to many HSPs), then filter out the best HSP based on score from my outfmt file (I use outfmt 6)? Versus just setting the -max_target_seqs and -max_hsps to 1 which essentially does the same thing?

I only need top hit and found that (at least for my samples), using default max target seqs just returned 100s of duplicates and never any different species matching to my query. Perhaps this is a case by case scenario?

Thanks!

Answer 1

[GenoMax]

Please read this note to understand the parameter you are referring to. If you are doing something qualitative then selecting 1 top hit may be fine but keep in mind that it may not be the only best hit in the dataset. With hsp you will be selecting one section of the subject sequence. Again may be fine for your intended use case.

There was a long discussion in a prior thread: Misunderstood parameter of NCBI BLAST