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Old 03-18-2013, 11:24 AM   #1
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Default Runtime of Bowtie

Hey everyone! Sorry if this is a repeat thread; I looked around for a bit, but I'm new so it's definitely possible I missed an answer to my question.

I'm interested in Bowtie's algorithm for read alignment (found here: Specifically, does anyone know, mathematically, how changing query length will affect the runtime of Bowtie? Likewise, how is Bowtie's speed affected by increased numbers of permitted mismatches? I've read and it's extremely helpful in answering these questions (there's a chart that compares Bowtie to other algorithms with respect to different read lengths, and I understand that allowing more mismatches will introduce excessive backtracking and potentially terminate the search), but I'm trying to get a better handle, mathematically, on what's going on here.

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