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:
-use_sw_tback 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
*** 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 :P
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, https://doi.org/10.1093/bioinformatics/btm585