PatternHunter

[…] an indicator of potential local similarity. it has been noticed first by [] that considering non-consecutive matches produces better results. the first similarity search program to use this idea was patternhunter [] where the distribution of the match positions is also optimized. if we denote a match by a 1 and a don't care position by a *, then the default seed of blast is 11111111111, […]

[…] 96 gb). it will be a great challenge for those laboratories without access to super-computers to analyze the huge hts metagenomic dataset by blastx against ncbi-nr approach., various tools, e.g. patternhunter , , blat , and blastz , have been developed for fast similarity searching. however, these tools more or less sacrificed searching sensitivity comparing with blast. one recently […]

[…] queries and the database are translated into the six possible potential proteins before searching. the translation time is not counted for the same reason as in tblastn. the speedup is shown in . , patternhunter [] which is implemented in java applies a novel seed model called “space seeds” to accelerate blast algorithm. this software can run on desktops. it is faster and more sensitive […]

[…] both the theoretical analysis and empirical experiments [,] have shown that choice of the seeding heuristics affects the sensitivity of local alignments. while blast requires consecutive matching, patternhunter [] allows spaced seeds, which can incorporate biological features of the underlying alignments. for example, spaced seeds designed for coding regions allow a mismatch following two […]

[…] seeds in the case of blast have been computed also using fasthc., sensitivity comparison with mandala, iedera, and speed (results from []). seeds were computed with the same parameters as those of patternhunter ii. fasthc (sensitivity values in bold) is the best in all cases. the sensitivity of the original seeds is significantly improved., sensitivity comparison with mandala, iedera, […]

[…] and then attempt to encode efficiently the differences between the instances of the repeat. the best compression to date for a single sequence is achieved by dnacompress []. this tool is based on patternhunter [] - a package for sequence homology search similar to blast. dnacompress runs patternhunter to find approximate repeats in the sequence, then sorts them such that long high similarity […]