I test edlib against usearch -usearch_gloal and vsearch --search_global, which is specifically designed for DNA database search based on global alignment. They use large gap open and extension penalities in sequences and small penalties at both ends, similar to HW mode in some sense but I get very different best hits after sorting by edit distance (sort by identity for usearch and vsearch). normally the best hit is the same while others are not among top 10. Which one is more close to the biological truth?
Hello Team,
I test edlib against usearch -usearch_gloal and vsearch --search_global, which is specifically designed for DNA database search based on global alignment. They use large gap open and extension penalities in sequences and small penalties at both ends, similar to HW mode in some sense but I get very different best hits after sorting by edit distance (sort by identity for usearch and vsearch). normally the best hit is the same while others are not among top 10. Which one is more close to the biological truth?
Thanks,
Jianshu