MSOAR: a high-throughput ortholog assignment system based on genome rearrangement. - MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. Background: Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (i.e., the random duplication model). However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (i.e., the tandem duplication model).

References in zbMATH (referenced in 6 articles )

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  1. You, Jie; Shi, Feng; Wang, Jianxin; Feng, Qilong: Fixed-parameter tractability for minimum tree cut/paste distance and minimum common integer partition (2020)
  2. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  3. Basavaraju, Manu; Panolan, Fahad; Rai, Ashutosh; Ramanujan, M. S.; Saurabh, Saket: On the kernelization complexity of string problems (2018)
  4. Shi, Guanqun; Zhang, Liqing; Jiang, Tao: MSOAR 2.0: incorporating tandem duplications into ortholog assignment based on genome rearrangement (2010) ioport
  5. Towfic, Fadi; Vanderplas, Susan; Oliver, Casey A.; Couture, Oliver; Tuggle, Christopher K.; Greenlee, M. Heather West; Honavar, Vasant: Detection of gene orthology from gene co-expression and protein interaction networks (2010) ioport
  6. Jiang, Tao: Some algorithmic challenges in genome-wide ortholog assignment (2009) ioport