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Title

Recent trends in Remote homology detection: an Indian Medley

 

Authors

Venkataraman S. Gowri1 and Sankaran Sandhya2*

 

Affiliation

1Molecular Biophysics Unit, Indian Institute of Science, Bangalore -560 012; 2National Centre for Biological Sciences, TIFR, GKVK campus, Bellary Road, Bangalore -560 065. Both authors contributed equally to this review.

 

E-mail*

sandhya@ncbs.res.in; * Corresponding author

 

Article Type

  

Current Trends

 

Date

  

received February 05, 2006; Accepted February 15, 2006; Published online February 21, 2006

 

Abstract

  

The development of remote homology detection methods is a challenging area in Bioinformatics. Sequence analysis-based approaches that address this problem have employed the use of profiles, templates and Hidden Markov Models (HMMs). These methods often face limitations due to poor sequence similarities and non-uniform sequence dispersion in protein sequence space. Search procedures are often asymmetrical due to over or under-representation of some protein families and outliers often remain undetected. Intermediate sequences that share high similarities with more than one protein can help overcome such problems. Methods such as MulPSSM and Cascade PSI-BLAST that employ intermediate sequences achieve better coverage of members in searches. Others employ peptide modules or conserved patterns of motifs or residues and are effective in overcoming dependencies on high sequence similarity to establish homology by using conserved patterns in searches. We review some of these recent methods developed in India in the recent past.

 

Keywords

  

Sequence analysis; Remote homology detection; PSI-BLAST; Protein Evolution

 

Citation

  

Gowri & Sandhya, Bioinformation 1(3): 94-96 (2006)

 

Edited by

  

N. Srinivasan

 

ISSN

 

0973-2063

 

Publisher

  

Biomedical Informatics

 

License

  

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.