Patternhunter Ii: Highly Sensitive and Fast Homology Search

Modern Homology Search

Dynamic programming [1] has full sensitivity, but too slow for large scale homology search. FASTA / BLAST type of heuristics [2] trade sensitivity for speed. Can we have both sensitivity and speed? We present the mathematical theory of optimized spaced seeds which allows modern homology search to achieve high sensitivity and high speed simultaneously. The spaced seed methodology is implemented ...

PatternHunter II 1 PatternHunter II : Highly Sensitive and Fast HomologySear

PatternHunter: faster and more sensitive homology search

MOTIVATION Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation. RESULTS We present a new homology search algorithm '...

A Sensitive Sequence Comparison Method

Biologists highly rely on good algorithms to find the homologous regions in bimolecular sequences. One advanced homology search program, PatternHunter, has been developed in 2002. Unlike the well-known program Blast using a consecutive model, it benefited from gapped (nonconsecutive) model to work better. By observing and analyzing some significant properties of gapped-models, we propose a new ...

Homology Search for Genes Using Biased HMMs

Motivation: Life science researchers often require an exhaustive list of protein coding genes similar to a given query gene. To find such genes, homology search tools, such as BLAST or PatternHunter, return a set of high-scoring pairs (HSPs). These HSPs then need to be correlated with existing sequence annotations, or assembled manually into putative gene structures. This process is error-prone...