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Open Access Highly Accessed Research article

Cgaln: fast and space-efficient whole-genome alignment

Ryuichiro Nakato12 and Osamu Gotoh13*

Author Affiliations

1 Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto-shi, Kyoto 606-8501, Japan

2 Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan

3 National Institute of Advanced Industrial Science and Technology, Computational Biology Research Center, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan

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BMC Bioinformatics 2010, 11:224  doi:10.1186/1471-2105-11-224

Published: 30 April 2010



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.


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 regions. In this paper, we present an update of the algorithm and the open-source program, Cgaln, that implements the algorithm. We compared the performance of Cgaln with those of other programs on whole genomic sequences of several bacteria and of some mammalian chromosome pairs. The results showed that Cgaln is several times faster and more memory-efficient than the best existing programs, while its sensitivity and accuracy are comparable to those of the best programs. Cgaln takes less than 13 hours to finish an alignment between the whole genomes of human and mouse in a single run on a conventional desktop computer with a single CPU and 2 GB memory.


Cgaln is not only fast and memory efficient but also effective in coping with genomic rearrangements. Our results show that Cgaln is very effective for comparison of large genomes, especially of intact chromosomal sequences. We believe that Cgaln provides novel viewpoint for reducing computational complexity and will contribute to various fields of genome science.