PMID- 15961499
OWN - NLM
STAT- In-Data-Review
DA  - 20050617
PUBM- Print
IS  - 1367-4803
VI  - 21 Suppl 1
DP  - 2005 Jun 1
TI  - ExonHunter: a comprehensive approach to gene finding.
PG  - i57-i65
AB  - MOTIVATION: We present ExonHunter, a new and comprehensive gene finding
      system that outperforms existing systems and features several new ideas
      and approaches. Our system combines numerous sources of information
      (genomic sequences, expressed sequence tags and protein databases of
      related species) into a gene finder based on a hidden Markov model in a
      novel and systematic way. In our framework, various sources of information
      are expressed as partial probabilistic statements about positions in the
      sequence and their annotation. We then combine these into the final
      prediction via a quadratic programming method, which we show to be an
      extension of existing methods. Allowing only partial statements is key to
      our transparent handling of missing information and coping with the
      heterogeneous character of individual sources of information. In addition,
      we give a new method for modeling the length distribution of intergenic
      regions in hidden Markov models. RESULTS: On a commonly used test set,
      ExonHunter performs significantly better than the existing gene finders
      ROSETTA, SLAM and TWINSCAN, with more than two-thirds of genes predicted
      completely correctly. AVAILABILITY: Supplementary material available at
      http://www.bioinformatics.uwaterloo.ca/supplements/05eh/ CONTACT:
      bbrejova@uwaterloo.ca.
AD  - School of Computer Science, University of Waterloo 200 University Avenue
      West, Waterloo, ON, Canada N2L 3G1.
FAU - Brejova, Brona
AU  - Brejova B
FAU - Brown, Daniel G
AU  - Brown DG
FAU - Li, Ming
AU  - Li M
FAU - Vinar, Tomas
AU  - Vinar T
LA  - eng
PT  - Journal Article
PL  - England
TA  - Bioinformatics
JID - 9808944
SB  - IM
EDAT- 2005/06/18 09:00
MHDA- 2005/06/18 09:00
AID - 21/suppl_1/i57 [pii]
AID - 10.1093/bioinformatics/bti1040 [doi]
PST - ppublish
SO  - Bioinformatics 2005 Jun 1;21 Suppl 1:i57-i65.

PMID- 15290755
OWN - NLM
STAT- MEDLINE
DA  - 20040803
DCOM- 20040917
LR  - 20041117
PUBM- Print
IS  - 0219-7200
VI  - 1
IP  - 4
DP  - 2004 Jan
TI  - Optimal spaced seeds for homologous coding regions.
PG  - 595-610
AB  - Optimal spaced seeds were developed as a method to increase sensitivity of
      local alignment programs similar to BLASTN. Such seeds have been used
      before in the program PatternHunter, and have given improved sensitivity
      and running time relative to BLASTN in genome-genome comparison. We study
      the problem of computing optimal spaced seeds for detecting homologous
      coding regions in unannotated genomic sequences. By using well-chosen
      seeds, we are able to improve the sensitivity of coding sequence alignment
      over that of TBLASTX, while keeping runtime comparable to BLASTN. We
      identify good seeds by first giving effective hidden Markov models of
      conservation in alignments of homologous coding regions. We give an
      efficient algorithm to compute the optimal spaced seed when conservation
      patterns are generated by these models. Our results offer the hope of
      improved gene finding due to fewer missed exons in DNA/DNA comparison, and
      more effective homology search in general, and may have applications
      outside of bioinformatics.
AD  - School of Computer Science, University of Waterloo, 200 University Ave
      West, Waterloo, ON N2L3G1, Canada. bbrejova@math.uwaterloo.ca
FAU - Brejova, Brona
AU  - Brejova B
FAU - Brown, Daniel G
AU  - Brown DG
FAU - Vinar, Tomas
AU  - Vinar T
LA  - eng
PT  - Journal Article
PL  - England
TA  - J Bioinform Comput Biol
JID - 101187344
RN  - 0 (Proteins)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - Algorithms
MH  - Animals
MH  - Comparative Study
MH  - Computational Biology
MH  - DNA/genetics
MH  - Drosophila/genetics
MH  - Humans
MH  - Markov Chains
MH  - Mice
MH  - Models, Statistical
MH  - Proteins/genetics
MH  - Research Support, Non-U.S. Gov't
MH  - Sensitivity and Specificity
MH  - Sequence Alignment/*statistics & numerical data
MH  - *Software
EDAT- 2004/08/04 05:00
MHDA- 2004/09/21 05:00
PHST- 2003/02/01 [received]
PHST- 2003/06/24 [accepted]
PHST- 2003/06/23 [revised]
AID - S0219720004000326 [pii]
PST - ppublish
SO  - J Bioinform Comput Biol 2004 Jan;1(4):595-610.