A PRACTICAL METHOD FOR MAXIMUM EXACT MATCHES IN LARGE GENOMES
Fursov M. Yu, D G Baksheyev, K V Rodionov, A A Golubitskii, D. V. Saraev, S. I. Denisov, Vladimir M. Blinov · 2004
Results: We describe a new fast and memory efficient indexing method for searching maximum exact matches in large genomes. The method is based on gapped suffix indexing and requires several times less memory and time than the traditional methods. With the gapped indexing, an interactive analysis of whole large genomes becomes executable on a desktop computer. The method serves as the basis for DPview, the system for searching, visualization and analysis of similarities in whole large genomes. Availability: http://bits.unipro.ru/eng/dpview.html