PatternHunter: faster and more sensitive homology search

By Bin Ma, John Tromp, Ming Li. Bioinform., 2002

950 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/57c4f040cbabb64f03f18bcaaab585c7e9a03bd9

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Citations in the corpus

Improved pairwise alignment of genomic dna (2007, methodology): “BLASTZ makes use of a specific 12-of-19 seed based on seed shown to be optimal for 64 bp homologies with 70% identity (Ma et al., 2002; Schwartz et al., 2003).”
Human-mouse alignments with BLASTZ. (2003, methodology): “Ma et al. (2002) propose looking for runs of 19 consecutive nucleotides in each sequence, within which the 12 positions indicated by a 1 in the string 1110100110010101111 are identical.”
De novo assembly of haplotype-resolved genomes with trio binning (2018, unknown): “Alternatively, the accuracy of long-read binning could be improved by more sophisticated classification (e.g. using spaced k-mers 48 ) or the integration of additional data types (e.g. Hi-C).”
Database resources of the National Center for Biotechnology Information (2014, methodology): “For rapid cross-species nucleotide queries, NCBI offers Discontiguous MegaBLAST, which uses a non-contiguous word match (55) as the nucleus for its alignments.”
Using quality scores and longer reads improves accuracy of Solexa read mapping (2008, background): “Research effort toward improving the structure of seeds used in these algorithms has also led to improvements in the algorithms themselves [11], and similar improvements might be observed by developing seeds specifically for the short read mapping problem.”
BLAST: at the core of a powerful and diverse set of sequence analysis tools (2004, background): “More sensitive is a search with discontiguous megaBLAST, which uses discontiguous word-matches (not all bases in a word are required to match) to initiate extensions ( 5 ,6).”
YASS: enhancing the sensitivity of DNA similarity search (2005, methodology): “Except for small sequences, the exact local alignment algorithm of Smith and Waterman (1) is not frequently used, and most alignments are obtained using heuristic alignment tools such as FASTA (2), FLASH (3), BLAST (4,5), BLASTZ (6) and PatternHunter (7,8).”
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (2009, background): “Spaced seeds have been shown to yield higher sensitivity than contiguous seeds of the same length [14,15].”