#29 · Genomics

Alignment-free tools replace pairwise search for remote homology and repeat discovery

The three items share a throughput-driven strategy: each avoids conventional pairwise nucleotide alignment in favor of a method-specific substitute. Riboseek uses di-mer based search for remote RNA/DNA similarity, reported as more sensitive than BLASTN and nhmmer and 250-376x faster, with a web server and 1.7M precomputed results. BWR-finder applies a BWT-based seed-and-extend approach to database-free de novo interspersed repeat detection in multi-gigabase genomes. AniAnn's uses alignment-free average nucleotide identity estimates to annotate tandem repeat arrays and satellite DNA boundaries. The common element is scalability rather than a shared algorithm. What is new is the extension of such substitutes to remote homology, de novo repeat discovery, and repeat boundary annotation.