Son K Pham1, Pavel A Pevzner. 1. Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA. kspham@cs.ucsd.edu
Abstract
MOTIVATION: The rapidly increasing set of sequenced genomes highlights the importance of identifying the synteny blocks in multiple and/or highly duplicated genomes. Most synteny block reconstruction algorithms use genes shared over all genomes to construct the synteny blocks for multiple genomes. However, the number of genes shared among all genomes quickly decreases with the increase in the number of genomes. RESULTS: We propose the Duplications and Rearrangements In Multiple Mammals (DRIMM)-Synteny algorithm to address this bottleneck and apply it to analyzing genomic architectures of yeast, plant and mammalian genomes. We further combine synteny block generation with rearrangement analysis to reconstruct the ancestral preduplicated yeast genome. CONTACT: kspham@cs.ucsd.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: The rapidly increasing set of sequenced genomes highlights the importance of identifying the synteny blocks in multiple and/or highly duplicated genomes. Most synteny block reconstruction algorithms use genes shared over all genomes to construct the synteny blocks for multiple genomes. However, the number of genes shared among all genomes quickly decreases with the increase in the number of genomes. RESULTS: We propose the Duplications and Rearrangements In Multiple Mammals (DRIMM)-Synteny algorithm to address this bottleneck and apply it to analyzing genomic architectures of yeast, plant and mammalian genomes. We further combine synteny block generation with rearrangement analysis to reconstruct the ancestral preduplicated yeast genome. CONTACT: kspham@cs.ucsd.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Anton Bankevich; Sergey Nurk; Dmitry Antipov; Alexey A Gurevich; Mikhail Dvorkin; Alexander S Kulikov; Valery M Lesin; Sergey I Nikolenko; Son Pham; Andrey D Prjibelski; Alexey V Pyshkin; Alexander V Sirotkin; Nikolay Vyahhi; Glenn Tesler; Max A Alekseyev; Pavel A Pevzner Journal: J Comput Biol Date: 2012-04-16 Impact factor: 1.479
Authors: Yu Lin; Jeffrey Yuan; Mikhail Kolmogorov; Max W Shen; Mark Chaisson; Pavel A Pevzner Journal: Proc Natl Acad Sci U S A Date: 2016-12-12 Impact factor: 11.205
Authors: Ksenia Krasheninnikova; Mark Diekhans; Joel Armstrong; Aleksei Dievskii; Benedict Paten; Stephen O'Brien Journal: Gigascience Date: 2020-06-01 Impact factor: 6.524