Protein function annotation based on ortholog clusters extracted from incomplete genomes using combinatorial optimization

Akshay Vashist, Casimir Kulikowski, Ilya Muchnik

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

Reliable automatic protein function annotation requires methods for detecting orthologs with known function from closely related species. While current approaches are restricted to finding ortholog clusters from complete proteomes, most annotation problems arise in the context of partially sequenced genomes. We use a combinatorial optimization method for extracting candidate ortholog clusters robustly from incomplete genomes. The proposed algorithm focuses exclusively on sequence relationships across genomes and finds a subset of sequences from multiple genomes where every sequence is highly similar to other sequences in the subset. We then use an optimization criterion similar to the one for finding ortholog clusters to annotate the target sequences. We report on a candidate annotation for proteins in the rice genome using ortholog clusters constructed from four partially complete cereal genomes - barley, maize, sorghum, wheat and the complete genome of Arabidopsis.

Original languageEnglish (US)
Title of host publicationResearch in Computational Molecular Biology - 10th Annual International Conference, RECOMB 2006, Proceedings
Pages99-113
Number of pages15
DOIs
StatePublished - Jul 14 2006
Event10th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2006 - Venice, Italy
Duration: Apr 2 2006Apr 5 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3909 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other10th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2006
CountryItaly
CityVenice
Period4/2/064/5/06

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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