Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
Paul Flicek
England
Research Article
Mining Unique-m Substrings from Genomes
Author(s): Kai Ye, Zhenyu Jia, Yipeng Wang, Paul Flicek and Rolf ApweilerKai Ye, Zhenyu Jia, Yipeng Wang, Paul Flicek and Rolf Apweiler
Unique substrings in genomes may indicate high level of specificity which is crucial and fundamental to many genetics studies, such as PCR, microarray hybridization, Southern and Northern blotting, RNA interference (RNAi), and genome (re)sequencing. However, being unique sequence in the genome alone is not adequate to guaranty high specificity. For example, nucleotides mismatches within a certain tolerance may impair specificity even if an interested substring occur only once in the genome. In this study we propose the concept of unique-m substrings of genomes for controlling specificity in genome-wide assays. A unique-m substring is defined if it only has a single perfect match on one strand of the entire genome while all other approximate matches must have more than m mismatches. We developed a pattern growth approach to systematically mine such unique-m substrings .. View More»
DOI:
10.4172/jpb.1000127