Does setting the -no_greedy switch make blastn behave like Smith-Waterman? The documentation states that the switch allows blast to "use non-greedy dynamic programming extension". It isn't clear to me what the impact of this switch will have. Does anyone know?
1 answer
BLAST will never behave like Smith-Waterman. This option is only applicable using megablast (searching for almost identical sequences), if I understood correctly it will skip the dynamic programming that follows the initial word matching and use greedy algorithm to extend the identical word.
I realize that it is supposed to work with megablast, I was just saying that it seems to run with blastn as well. Also, it isn't completely true that BLAST will never behave like SW, BLASTP has a flag that forces SW alignments. That is sort of what I'm confused about here: I don't think it is causing megablast to behave like SW, but it is changing the way alignments are generated.
Log in to answer this question.
-
Bioinformatics recursion practical applications
written by R.T. Canterbury •
-
Problem using Biopython qblast (NCBIWWW) with refseq_genomic database
written by Spencer D. •
-
Tips to download pathway information from anywhere (but KEGG)?
written by fr
-
is there a way to get splice sites from BLAST results?
written by wrf •
-
Convert MEDIP-seq RMS values into AMS using MEDIP
written by rdbcasillas11 •
-
BLAST definition and difference between 'qcovs' and 'qcovhsp'
written by rwn
-
Missing BLAST hits - max_hsps and max_target_seqs?
written by glenn •
-
Use of ebPatterns for EBcoexpress package for differential coexpression analysis
written by oganm
-
blast FATAL ERROR: BlastFormattingInfoNew returned non-z
written by rotmus0 •
-
another gkno install pb
written by bouleste •
