tPatternHunter: gapped, fast and sensitive translated homology search
نویسندگان
چکیده
UNLABELLED New ideas, spaced seeds and gapped alignment before 6-frame translation are implemented for translated homology search in tPatternHunter. The new software compares favorably with tBLASTx. AVAILABILITY The software is free to academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/ CONTACT [email protected].
منابع مشابه
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 ...
متن کاملFast filtering for RNA homology search
MOTIVATION Homology search for RNAs can use secondary structure information to increase power by modeling base pairs, as in covariance models, but the resulting computational costs are high. Typical acceleration strategies rely on at least one filtering stage using sequence-only search. RESULTS Here we present the multi-segment CYK (MSCYK) filter, which implements a heuristic of ungapped stru...
متن کاملHighly Sensitive Homology Search Methods on Parallel Computer
We have developed two kinds of highly sensitive homology search methods based on SmithWaterman-like algorithm. One is direct comparison between DNA sequence and amino acid sequence. The other is comparison between DNA sequences through translated amino acid sequences. Both methods consider gaps in amino acid and nucleotide sequence levels simultaneously. Although these methods attain higher sen...
متن کاملQuick, Practical Selection of Effective Seeds for Homology Search
It has been observed that in homology search gapped seeds have better sensitivity than ungapped ones for the same cost (weight). In this paper, we propose a probability leakage model (a dissipative Markov system) to elucidate the mechanism that confers power to spaced seeds. Based on this model, we identify desirable features of gapped search seeds and formulate an extremely efficient procedure...
متن کاملPatternhunter Ii: Highly Sensitive and Fast Homology Search
Extending the single optimized spaced seed of PatternHunter to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle.
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bioinformatics
دوره 21 4 شماره
صفحات -
تاریخ انتشار 2005