I need to blastp a genome (15,000 seqs) against genome (12,000 seqs) using Biopython. I decided to use local blast and query genome 1 fasta file against genome 2 database ( made by makeblastdb command with second genome fast file ). I also managed to perform the blast search for default parameters of standalone blastp. However, when I try to change word size to BIGGER value ( default is 3 and i set it to 6, the blast performs extremely slow. I am kind of confused why such a thing happens because increasing word size is supposed to make things go faster. Here is how i pass arguments to NcbiblastpCommandline function:
NcbiblastpCommandline( word_size=6, query=queryInputPath, db=subjectInputPath, out=outputPath, outfmt=5 )()
things are much faster when the function does not have 'word_size=6' keyword argument. Without word size = 6 it takes around an 1,5 h to perform blast. My mac has 4gb of RAM and 1,6 GHz Intel Core i5 processor. What may be the cause?