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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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Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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