I'm trying to recreate the BLASTP parameters -F "m S" -s F (representing soft-filtering and smith waterman final alignment) from the paper below. However, I'm using BLAST+ v 2.10.1 and it looks like all the parameters are different.

Can someone confirm that the above parameter settings are analogous to running BLAST+ with -soft_masking True -use_sw_tback? i.e. is -use_sw_tback the same as -s F and is -soft_masking True the same as -F "m S"? I'm suggesting -use_sw_tback as it's literally the only flag description I can see that mentions smith-waterman:

   Compute locally optimal Smith-Waterman alignments?

Also, I'm not sure if I should be including -seg yes with the BLASTP options - is seg what provides the locations mentioned for soft_masking below?

*** Query filtering options
-seg <String>
  Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
  'no' to disable)
  Default = `no'
-soft_masking <Boolean>
  Apply filtering locations as soft masks
  Default = `false'

Lastly, in general, I'm not sure if query soft-masking, potentially including seg, requires the database to be masked as well. I assume they are completely separate?

Thanks for reading what has become a slight stream of consciousness, much appreciated 😛

paper 1:
Gabriel Moreno-Hagelsieb, Kristen Latimer, Choosing BLAST options for better detection of orthologs as reciprocal best hits, Bioinformatics, Volume 24, Issue 3, 1 February 2008, Pages 319–324, doi.org/10.1093/bioinformatics/btm585

Source link