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I have been using BLAST to compare genome sequences with the goal of identifying genomic regions that are unique to specific fungal strains. Unfortunately, BLAST misses a large number of long (>1 kb), almost perfect alignments, resulting in too many false positives for my liking. Can anyone recommend another alignment tool that does not miss obvious matches? I know Smith Waterman is more sensitive but I'd like something a little more computationally efficient.
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Try turning off the low complexity filter - if part of your query triggers this, that part won't be used in the searches. -
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I routinely switch off the low complexity filter, so this is not the issue. The problem lies in the initial blast step - breaking the query into short seed "words." Presumably, for long queries, such as genomic contigs, the distribution of the seeds is too sparse.Comment
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