BLAST options: max_target_seqs and num_alignments

Question

[biolab]

Hi everyone,

Could anyone explain in a little bit more details what's the difference for the options max_target_seqs and num_alignments. If I only want the top hit, how to do in BLAST setting?

Thank you very much!

Answer 1

[Siva]

It depends on what value you set for the option outfmt (options range from 0 to 12) and you can only use either one of the max_target_seqs or num_alignments options.

If you want only one hit:

• If you set outfmt to any option <=4, set both -num_descriptions and -num_alignments to 1
• If you set outfmt to any option >4, set -max_target_seqs to 1

I hope you are aware that if you want only the top hit and if your query sequence is in the database you are searching against ('nr' for example), your query sequence might be the top hit.

[kamiljaron]

I am afraid that is not what max_target_seqs does: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166

[Peter]

See https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-repartee-one.html and https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-repartee-two.html for more details - all of -max_target_seqs, -num_descriptions and -num_alignments set an internal limit during the search as well as limiting the output.

[biolab]

Thank you, Siva. Your comment is really helpful.