Tweet
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
-
Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...09-23-2024, 06:35 AM -
During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.
Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...09-09-2024, 10:59 AM
Comment