GAME: A simple and efficient whole genome alignment method using maximal exact match filtering

Jeong Hyeon Choi, Hwan Gue Cho, Sun Kim

Research output: Contribution to journalArticle

15 Scopus citations


In this paper, we present a simple and efficient whole genome alignment method using maximal exact match (MEM). The major problem with the use of MEM anchor is that the number of hits in non-homologous regions increases exponentially when shorter MEM anchors are used to detect more homologous regions. To deal with this problem, we have developed a fast and accurate anchor filtering scheme based on simple match extension with minimum percent identity and extension length criteria. Due to its simplicity and accuracy, all MEM anchors in a pair of genomes can be exhaustively tested and filtered. In addition, by incorporating the translation technique, the alignment quality and speed of our genome alignment algorithm have been further improved. As a result, our genome alignment algorithm, GAME (Genome Alignment by Match Extension), performs competitively over existing algorithms and can align large whole genomes, e.g., A. thaliana, without the requirement of typical large memory and parallel processors. This is shown using an experiment which compares the performance of BLAST, BLASTZ, PatternHunter, MUMmer and our algorithm in aligning all 45 pairs of 10 microbial genomes. The scalability of our algorithm is shown in another experiment where all pairs of five chromosomes in A. thaliana were compared.

Original languageEnglish (US)
Pages (from-to)244-253
Number of pages10
JournalComputational Biology and Chemistry
Issue number3
Publication statusPublished - Jun 1 2005
Externally publishedYes



  • Anchor filtering
  • Maximal exact match
  • Whole genome alignment

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics

Cite this