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.
-
-
Try turning off the low complexity filter - if part of your query triggers this, that part won't be used in the searches. -
-
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
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment