Cgaln: fast and space-efficient whole-genome alignment

Background: Whole-genome sequence alignment is an essential process for extracting valuable information about the functions, evolution, and peculiarities of genomes under investigation. As available genomic sequence data accumulate rapidly, there is great demand for tools that can compare whole-genome sequences within practical amounts of time and space. However, most existing genomic alignment tools can treat sequences that are only a few Mb long at once, and no state-of-the-art alignment program can align large sequences such as mammalian genomes directly on a conventional standalone computer. Results: We previously proposed the CGAT (Coarse-Grained AlignmenT) algorithm, which performs an alignment job in two steps: first at the block level and then at the nucleotide level. The former is "coarse-grained" alignment that can explore genomic rearrangements and reduce the sizes of the regions to be analyzed in the next step. The latter is detailed alignment within limited regi...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Ryuichiro Nakato, Osamu Gotoh
• Keywords: BMCBI 2010, Genomic, Sequences, Whole-genome Sequences