iRO-3wPseKNC: Identify DNA replication origins by three-window-based PseKNC

Bin Liu*, Fan Weng, De Shuang Huang, Kuo Chen Chou

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

102 Citations (Scopus)

Abstract

Motivation: DNA replication is the key of the genetic information transmission, and it is initiated from the replication origins. Identifying the replication origins is crucial for understanding the mechanism of DNA replication. Although several discriminative computational predictors were proposed to identify DNA replication origins of yeast species, they could only be used to identify very tiny parts (250 or 300 bp) of the replication origins. Besides, none of the existing predictors could successfully capture the ‘GC asymmetry bias’ of yeast species reported by experimental observations. Hence it would not be surprising why their power is so limited. To grasp the CG asymmetry feature and make the prediction able to cover the entire replication regions of yeast species, we develop a new predictor called ‘iRO-3wPseKNC’. Results: Rigorous cross validations on the benchmark datasets from four yeast species (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis and Pichia pastoris) have indicated that the proposed predictor is really very powerful for predicting the entire DNA duplication origins.

Original languageEnglish
Pages (from-to)3086-3093
Number of pages8
JournalBioinformatics
Volume34
Issue number18
DOIs
Publication statusPublished - 15 Sept 2018
Externally publishedYes

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Liu, B., Weng, F., Huang, D. S., & Chou, K. C. (2018). iRO-3wPseKNC: Identify DNA replication origins by three-window-based PseKNC. Bioinformatics, 34(18), 3086-3093. https://doi.org/10.1093/bioinformatics/bty312