Similarity search tool | Command line parameter |
---|---|
NCBI BLAST | blastall -p blastn -i QUERY -d SUBJECT -m 7 -a 1 -S 3 -e 10 -F ‘m D’ -b 100000 |
WU-BLAST | blastn SUBJECT QUERY mformat=7 cpus=1 E=10 wordmask=dust B=100000 hspmax=100000 hspsepSmax=50 hspsepQmax=50 |
BLAT | blat SUBJECT QUERY OUTFILE -t=dna -q=dna -out=blast -minScore=30 -minIdentity=50 |
BLASTZ | blastz QUERY SUBJECT B=2 C=2 K=3500 Y=700 |
Mummer | mummer -b -c -F -l 44 -mum SUBJECT QUERY |