Multiple hits from BLAT?

[thsuk1]

Hi guys,

Is there any option of BLAT to find multiple hits of one query? The name of BLAT is 'blast like alignment tool' so I thought it would produce multiple hits.

[cliffbeall]

In my hands it gives multiple hits, if they exist. Maybe your query only matches one sequence in the target?

[Torst]

I agree with cliffbeall - it will list multiple hits if they exist.

Perhaps use the -out=blast option to get a traditional BLAST output file.