Hello.

I am currently trying to match a large set of DNA sequences (~10,000 sequences, ~20 bp each) to the entire human pre-mRNA, looking only for exact matches. Most methods I've used have been far too slow, until I found Bowtie. After indexing the pre-mRNA (took a few hours) it can do the matching in a few minutes. However, it only finds ~60% of the possible matches, even with the -a flag. Is there a way to find all matches with Bowtie (possibly sacrificing some of its speed) or is incomplete sensitivity just a drawback of the algorithm that allows the impressive speed?

I have read the Bowtie paper, but unfortunately I don't quite understand every part of the algorithm.

Thanks!