Parallel Position Weight Matrices algorithms
نویسندگان
چکیده
منابع مشابه
Large Scale Matching for Position Weight Matrices
This paper addresses the problem of multiple pattern matching for motifs encoded by Position Weight Matrices. We first present an algorithm that uses a multi-index table to preprocess the set of motifs, allowing a dramatically decrease of computation time. We then show how to take benefit from simlar motifs to prevent useless computations.
متن کاملEnhanced position weight matrices using mixture models
MOTIVATION Positional weight matrix (PWM) is derived from a set of experimentally determined binding sites. Here we explore whether there exist subclasses of binding sites and if the mixture of these subclass-PWMs can improve the binding site prediction. Intuitively, the subclasses correspond to either distinct binding preference of the same transcription factor in different contexts or distinc...
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Recently, hierarchically semiseparable (HSS) matrices have been used in the development of fast direct sparse solvers. Key applications of HSS algorithms, coupled with multifrontal solvers, appear in solving certain large-scale computational inverse problems. Here, we develop massively parallel HSS algorithms appearing in these solution methods, namely, parallel HSS construction using the rank ...
متن کاملLearning position weight matrices from sequence and expression data.
Position weight matrices (PWMs) are widely used to depict the DNA binding preferences of transcription factors (TFs) in computational molecular biology and regulatory genomics. Thus, learning an accurate PWM to characterize the binding sites of a specific TF is a fundamental problem that plays an important role in modeling regulatory motifs and discovering the binding targets of TFs. Given a se...
متن کاملFast Search Algorithms for Position Specific Scoring Matrices
Fast search algorithms for finding good instances of patterns given as position specific scoring matrices are developed, and some empirical results on their performance on DNA sequences are reported. The algorithms basically generalize the Aho–Corasick, filtration, and superalphabet techniques of string matching to the scoring matrix search. As compared to the naive search, our algorithms can b...
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ژورنال
عنوان ژورنال: Parallel Computing
سال: 2011
ISSN: 0167-8191
DOI: 10.1016/j.parco.2010.10.001