Efficient combination of multiple word models for improved sequence comparison.
BACKGROUND
Studies of efficient and sensitive sequence comparison methods are driven by a need to find homologous regions of weak similarity between large genomes.


RESULTS
We describe an improved method for finding similar regions between two sets of DNA sequences. The new method generalizes existing methods by locating word matches between sequences under two or more word models and extending word matches into high-scoring segment pairs (HSPs). The method is implemented as a computer program named DDS2. Experimental results show that DDS2 can find more HSPs by using several word models than by using one word model.


BACKGROUND
The DDS2 program is freely available for academic use in binary code form at http://bioinformatics.iastate.edu/aat/align/align.html and in source code form from the corresponding author.
Huang
Xiaoqiu
X
Department of Computer Science, Iowa State University, Ames, IA 50011-1040, USA. xqhuang@cs.iastate.edu
Ye
Liang
L
Chou
Hui-Hsien
HH
Yang
I-Hsuan
IH
Chao
Kun-Mao
KM
D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software