Using functionally important sites to identify orthologous relations

Hsuan Chao Chiu, Yuh-Jyh Hu

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

Abstract

Making accurate functional predictions for genes plays an important role in the era of proteomics. The most reliable functional information is extracted from orthologs in other species when annotating an unknown gene. Here a site-based approach is proposed to predict orthologous relations. The method first identifies important sites that confer specificity of paralogs in the multiple sequence alignment of homologous proteins. It then predicts orthologous relations for unannotated proteins based on the important sites found. When applied to the bacterial transcription factor PurR/LacI family and the protein kinase AGC group family, our method was able to identify, with few false positives, the important sites that agree with those obtained from biological experiments. We also tested it on the AGC group family, the α-proteasome family, the glycoprotein hormone family and the growth hormone family to demonstrate its ability to predict orthologs. Compared with other prediction methods based on phylogenetic analysis or hidden Markov models, our method not only has competitive prediction accuracy, but also provides valuable biological information of important sites associated with orthologs which can be further studied in biological experiments.

Original languageEnglish
Title of host publicationProceedings - IEEE 5th International Symposium on Multimedia Software Engineering, ISMSE 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages265-272
Number of pages8
ISBN (Electronic)0769520316, 9780769520315
DOIs
StatePublished - 1 Jan 2003
Event5th IEEE International Symposium on Multimedia Software Engineering, ISMSE 2003 - Taichung, Taiwan
Duration: 10 Dec 200312 Dec 2003

Publication series

NameProceedings - IEEE 5th International Symposium on Multimedia Software Engineering, ISMSE 2003

Conference

Conference5th IEEE International Symposium on Multimedia Software Engineering, ISMSE 2003
CountryTaiwan
CityTaichung
Period10/12/0312/12/03

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  • Cite this

    Chiu, H. C., & Hu, Y-J. (2003). Using functionally important sites to identify orthologous relations. In Proceedings - IEEE 5th International Symposium on Multimedia Software Engineering, ISMSE 2003 (pp. 265-272). [1254451] (Proceedings - IEEE 5th International Symposium on Multimedia Software Engineering, ISMSE 2003). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/MMSE.2003.1254451