Mining the Arabidopsis and rice genomes for cyclophilin protein families

S. O. Opiyo, E. N. Moriyama

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Cyclophilins, which possess peptidyl-prolyl isomerase activity, are cellular targets of immunosuppressant drugs and involved in a wide variety of functions. While the Arabidopsis thaliana genome contains the largest number of cyclophilins, the number of plant cyclophilins available in databases is small compared to that of other organisms. It implies that many cyclophilins are yet to be identified in plants. In order to identify cyclophilin candidates from available plant sequence data, we examined alignment-free methods based on Partial Least Squares (PLS). PLS classifier performed better than profile hidden Markov models and PSI-BLAST in identifying cyclophilins from the Arabidopsis and rice genomes.

Original languageEnglish (US)
Pages (from-to)295-309
Number of pages15
JournalInternational Journal of Bioinformatics Research and Applications
Volume5
Issue number3
DOIs
StatePublished - Jun 1 2009

Fingerprint

Cyclophilins
Arabidopsis
Genes
Genome
Proteins
Hidden Markov models
Classifiers
Least-Squares Analysis
Peptidylprolyl Isomerase
Immunosuppressive Agents
Oryza
Databases
Pharmaceutical Preparations

Keywords

  • Bioinformatics
  • Cyclophilins
  • PLS
  • Partial least squares
  • Profile hidden Markov model

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Clinical Biochemistry
  • Health Information Management

Cite this

Mining the Arabidopsis and rice genomes for cyclophilin protein families. / Opiyo, S. O.; Moriyama, E. N.

In: International Journal of Bioinformatics Research and Applications, Vol. 5, No. 3, 01.06.2009, p. 295-309.

Research output: Contribution to journalArticle

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