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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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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