In blastp given in the blast wrapper used for the BLASTp baseline, a word_size of 11 is given as a default. While this is the default value for blastn, blastp-short, as used in the code, installed with the ncbi-blast+ package, only supports a max word_size of 7.
For every application in the paper the actual word_size should be provided, as this setting has quite an impact in the BLAST results. Alternatively, there is a blastp installation that does support a word_size of 11, and if so, I would be interested which installation that would be.
In
blastpgiven in the blast wrapper used for the BLASTp baseline, aword_sizeof 11 is given as a default. While this is the default value forblastn,blastp-short, as used in the code, installed with the ncbi-blast+ package, only supports a maxword_sizeof 7.For every application in the paper the actual word_size should be provided, as this setting has quite an impact in the BLAST results. Alternatively, there is a blastp installation that does support a
word_sizeof 11, and if so, I would be interested which installation that would be.