Murasaki: A fast, parallelizable algorithm to find anchors from multiple genomes

Kris Popendorf, Hachiya Tsuyoshi, Yasunori Osana, Yasubumi Sakakibara

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Background:With the number of available genome sequences increasing rapidly, the magnitude of sequence data required for multiple-genome analyses is a challenging problem. When large-scale rearrangements break the collinearity of gene orders among genomes, genome comparison algorithms must first identify sets of short well-conserved sequences present in each genome, termed anchors. Previously, anchor identification among multiple genomes has been achieved using pairwise alignment tools like BLASTZ through progressive alignment tools like TBA, but the computational requirements for sequence comparisons of multiple genomes quickly becomes a limiting factor as the number and scale of genomes grows. Methodology/Principal Findings: Our algorithm, named Murasaki, makes it possible to identify anchors within multiple large sequences on the scale of several hundred megabases in few minutes using a single CPU. Two advanced features of Murasaki are (1) adaptive hash function generation, which enables efficient use of arbitrary mismatch patterns (spaced seeds) and therefore the comparison of multiple mammalian genomes in a practical amount of computation time, and (2) parallelizable execution that decreases the required wall-clock and CPU times. Murasaki can perform a sensitive anchoring of eight mammalian genomes (human, chimp, rhesus, orangutan, mouse, rat, dog, and cow) in 21 hours CPU time (42 minutes wall time). This is the first single-pass in-core anchoring of multiple mammalian genomes. We evaluated Murasaki by comparing it with the genome alignment programs BLASTZ and TBA. We show that Murasaki can anchor multiple genomes in near linear time, compared to the quadratic time requirements of BLASTZ and TBA, while improving overall accuracy. Conclusions/Significance: Murasaki provides an open source platform to take advantage of long patterns, cluster computing, and novel hash algorithms to produce accurate anchors across multiple genomes with computational efficiency significantly greater than existing methods. Murasaki is available under GPL at http://murasaki.sourceforge.net.

Original languageEnglish
Article numbere12651
JournalPLoS One
Volume5
Issue number9
DOIs
Publication statusPublished - 2010

Fingerprint

Anchors
Genes
Genome
genome
Program processors
Pongo
Gene Order
Cluster computing
Conserved Sequence
Pongo pygmaeus
conserved sequences
Human Genome
Hash functions
Computational efficiency
Seeds
Seed
Rats
Clocks
Dogs

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Murasaki : A fast, parallelizable algorithm to find anchors from multiple genomes. / Popendorf, Kris; Tsuyoshi, Hachiya; Osana, Yasunori; Sakakibara, Yasubumi.

In: PLoS One, Vol. 5, No. 9, e12651, 2010.

Research output: Contribution to journalArticle

Popendorf, Kris ; Tsuyoshi, Hachiya ; Osana, Yasunori ; Sakakibara, Yasubumi. / Murasaki : A fast, parallelizable algorithm to find anchors from multiple genomes. In: PLoS One. 2010 ; Vol. 5, No. 9.
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