Academic databases and citation indexes like Google Scholar or PubMed

LexicMap Aligns 30k Hits in 1 Minute, Advancing Genomic Research

Sep 2, 2024, 04:05 PM

LexicMap is a newly developed sequence alignment tool designed to efficiently handle queries against millions of prokaryotic genomes. LexicMap allows for full alignment of bacterial and archaeal data, with the capability to perform alignments with higher sensitivity as query divergence decreases from 90% to 80% for queries of 1 kb or more. The tool can align a single gene against 2.34 million prokaryotic genomes from GenBank and RefSeq in a time frame ranging from 36 seconds for rare genes to 15 minutes for 16S RNA genes. A key feature of LexicMap is its use of a small set of probe k-mers to efficiently index the database, enabling fast and low-memory alignment processes. Notably, it can search for a gene with over 30,000 hits against 2 million bacterial genomes within 1 minute. The development of LexicMap is expected to have a substantial impact on advancing microbial genomics research.