pass perameters to blast?

mhahsler / rBLAST

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

GNU General Public License v3.0

103 stars 22 forks source link

pass perameters to blast? #21

Closed philtat closed 7 months ago

philtat commented 2 years ago

Is it possible to pass alignment parameters to blast using this program? For example specifying word_size.

mhahsler commented 2 years ago

The parameter BLAST_args in predict can be used to pass on additional parameters to the program. See ? blast. I assume that also lets you specify alignment parameters.

rocketeer1998 commented 1 year ago

I faced the same issue. I'd like to change the BLAST algorithm to Somewhat similar sequences (blastn) as shown in BLAST webpage(https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome), so I can show the whole results without percentage cutoff. Any ideas? Thanks a lot!

rocketeer1998 commented 1 year ago

Answer to myself. query_blast <- predict(bl, seq[1:length(seq),], BLAST_args = c("-task blastn","-perc_identity 80")). All parameters can be passed to BLAST_args. Options can be found in BLAST command line user manual, 'https://www.animalgenome.org/bioinfo/resources/manuals/blast2.2.24/user_manual.pdf'.