PatternHunter

[…] reads are required. surprisingly, megablast with contiguous seeds performs better than discontiguous seed megablast and blastz for alignment of ovine reads to the equine and bovine genomes. patternhunter would perform much better if it were able to effectively utilise soft masking. a range of programs and parameter settings can be quickly surveyed with datasets appropriate […]

[…] [3] and blast [4] and including specific methods for protein similarities such as blastp [5]. seed-based heuristics were recently enhanced by advanced seeding tools like the spaced seeds used in patternhunter [6] or yass [7] (see [8] for a recent survey). authors of this paper also worked on the alliance between advanced seeds techniques and reconfigurable architectures [9]., the main idea […]