NDLI: Identifying positional homologs as bidirectional best hits of sequence and gene context similarity

Content Provider	IEEE Xplore Digital Library
Author	Zhang, M. Hon Wai Leong
Copyright Year	2011
Description	Author affiliation: Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore 117417 (Zhang, M.; Hon Wai Leong)
Abstract	Identifying corresponding genes (orthologs) in different species is an important step in genome-wide comparative analysis. In particular, one-to-one correspondences between genes in different species greatly simplify certain problems such as transfer of function annotation and genome rearrangement studies. Positional homologs are the direct descendants of a single ancestral gene in the most recent common ancestor and by definition form one-to-one correspondence. In this work, we present a simple yet effective method (BBH-LS) for the identification of positional homologs from the comparative analysis of two genomes. Our BBH-LS method integrates sequence similarity and gene context similarity in order to get more accurate ortholog assignments. Specifically, BBH-LS applies the bidirectional best hit heuristic to a combination of sequence similarity and gene context similarity scores. We applied our method to the human, mouse, and rat genomes and found that BBH-LS produced the best results when using both sequence and gene context information equally. Compared to the state-of-the-art algorithms, such as MSOAR2, BBH-LS is able to identify more positional homologs with fewer false positives.
Starting Page	117
Ending Page	122
File Size	762995
Page Count	6
File Format	PDF
ISBN	9781457716614
e-ISBN	9781457716669
e-ISBN	9781457716652
DOI	10.1109/ISB.2011.6033141
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-09-02
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Context Peptides Systems biology Genomics Humans Mice Bioinformatics
Content Type	Text
Resource Type	Article

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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