منابع مشابه
Vector seeds: An extension to spaced seeds
We present improved techniques for finding homologous regions in DNA and protein sequences. Our approach focuses on the core regions of a local pairwise alignment; we suggest new ways to characterize these regions that allow marked improvements in both specificity and sensitivity over existing techniques for sequence alignment. For any such characterization, which we call a vector seed, we give...
متن کاملSpaced Seeds Design Using Perfect Rulers
We consider the problem of lossless spaced seed design for approximate pattern matching. We show that, using mathematical objects known as perfect rulers, we can derive a family of spaced seeds for matching with up to two errors. We analyze these seeds with respect to the trade-off they offer between seed weight and the minimum length of the pattern to be matched. We prove that for patterns of ...
متن کاملOn spaced seeds for similarity search
Genomics studies routinely depend on similarity searches based on the strategy of finding short seed matches (contiguous k bases) which are then extended. The particular choice of the seed length, k, is determined by the tradeoff between search speed (larger k reduces chance hits) and sensitivity (smaller k finds weaker similarities). A novel idea of using a single deterministic optimized space...
متن کاملOptimal Spaced Seeds for Homologous Coding Regions
Optimal spaced seeds were developed as a method to increase sensitivity of local alignment programs similar to BLASTN. Such seeds have been used before in the program PatternHunter, and have given improved sensitivity and running time relative to BLASTN in genome-genome comparison. We study the problem of computing optimal spaced seeds for detecting homologous coding regions in unannotated geno...
متن کاملMetagenomic reads binning with spaced seeds
Article history: Received 23 February 2017 Received in revised form 16 May 2017 Accepted 21 May 2017 Available online xxxx
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ژورنال
عنوان ژورنال: Journal of Computer and System Sciences
سال: 2005
ISSN: 0022-0000
DOI: 10.1016/j.jcss.2004.12.008