Computing Reviews
Today's Issue Hot Topics Search Browse Recommended My Account Log In
Review Help
Search
Evidence combination in hidden Markov models for gene predictionBrejova B.2006Type:Doctoral Thesis
Date Reviewed: Mar 26 2007

In this significant thesis, the author studies two fundamental problems of genomic sequence analysis: gene finding and homology search. The work is organized into four chapters.

The author introduces new techniques for finding genes in genomic sequences, using sequence similarity information, and a flexible framework for combining multiple sources of evidence in gene finding. This work generalizes existing methods for combining complete probability statements to the case of partial statements.

The thesis discusses the problem of finding similar sequences in large sequence databases by improving a popular algorithm using probabilistic models of target sequence similarities. This leads to the finding of more useful evidence for gene finding. It constructs spaced seeds that significantly increase the number of homologous coding regions, and improve the accuracy and running time of similarity search in protein coding regions.

ExonHunter, the gene finder developed in the thesis, combines evidence from proteins, expressed sequence tags (ESTs), and genome alignments. These are tested on human and fruit fly genomic sequences. This gene finder outperforms other gene finders that use only genomic alignments as a source of information.

The thesis introduces hidden Markov models, to form the basis of the gene finder, and to model the properties of sequence similarities.

This study will be of interest to those researching transmembrane protein topology, protein secondary structure prediction, and components of homology.

Reviewer:  P.R. Parthasarathy Review #: CR134076
Bookmark and Share
  Reviewer Selected
 
 
Markov Processes (G.3 ... )
 
 
Biology And Genetics (J.3 ... )
 
 
Heuristic Methods (I.2.8 ... )
 
 
Probabilistic Algorithms (Including Monte Carlo) (G.3 ... )
 
 
Problem Solving, Control Methods, And Search (I.2.8 )
 
 
Life And Medical Sciences (J.3 )
 
  more  
Would you recommend this review?
yes
no
Other reviews under "Markov Processes": Date
Continuous-time Markov chains and applications
Yin G., Zhang Q., Springer-Verlag New York, Inc., New York, NY, 1998. Type: Book (9780387982441)
Jan 1 1999
Stochastic dynamic programming and the control of queueing systems
Sennott L., Wiley-Interscience, New York, NY, 1999. Type: Book (9780471161202)
Jan 1 1999
Lower bounds for randomized mutual exclusion
Kushilevitz E., Mansour Y., Rabin M., Zuckerman D. SIAM Journal on Computing 27(6): 1550-1563, 1998. Type: Article
Jul 1 1999
more...

E-Mail This Printer-Friendly
Send Your Comments
Contact Us
Reproduction in whole or in part without permission is prohibited.   Copyright 1999-2024 ThinkLoud®
Terms of Use
| Privacy Policy