Prediction of orthologous relationship by functionally important sites

Hsuan Chao Chiu, C. Allen Chang, Yuh-Jyh Hu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Making accurate functional predictions plays an important role in the era of proteomics. Reliable functional information can be extracted from orthologs in other species when annotating an unknown gene. Here a site-based approach called PORFIS is proposed to predict orthologous relationship. When applied to the bacterial transcription factor PurR/LacI family and the protein kinase AGC family, our method was able to identify, with few false positives, the important sites that agree with those verified by biological experiments. We also tested it on the α-proteasome family, the glycoprotein hormone family and the growth hormone family to demonstrate its ability to predict orthologous relationship. Compared with other prediction methods based on phylogenetic analysis or hidden Markov models, PORFIS not only has competitive prediction accuracy, but also provides valuable biological information of functionally important sites associated with orthologs which can be further studied in biological experiments.

Original languageEnglish
Pages (from-to)209-222
Number of pages14
JournalComputer Methods and Programs in Biomedicine
Issue number3
StatePublished - 1 Jun 2005


  • Important sites
  • Orthologs
  • Paralogs
  • Protein functions

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