Large Scale Matching for Position Weight Matrices
نویسندگان
چکیده
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.
منابع مشابه
Centralized Clustering Method To Increase Accuracy In Ontology Matching Systems
Ontology is the main infrastructure of the Semantic Web which provides facilities for integration, searching and sharing of information on the web. Development of ontologies as the basis of semantic web and their heterogeneities have led to the existence of ontology matching. By emerging large-scale ontologies in real domain, the ontology matching systems faced with some problem like memory con...
متن کاملMOODS: fast search for position weight matrix matches in DNA sequences
UNLABELLED MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for ...
متن کاملDiscovering sequence motifs of different patterns parallel using DNA operations
Discovery of motifs in biological sequences and various types of subsequences in commercial databases have varied applications and interpretations. This paper proposes a new approach to solve the Combinatorial Pattern Matching (CPM), search for continuous and gapped rigid subsequences and discover Longest Common Rigid Subsequences (LCRS) from the given sequences using DNA operations and modifie...
متن کاملOptimized Position Weight Matrices in Prediction of Novel Putative Binding Sites for Transcription Factors in the Drosophila melanogaster Genome
Position weight matrices (PWMs) have become a tool of choice for the identification of transcription factor binding sites in DNA sequences. DNA-binding proteins often show degeneracy in their binding requirement and thus the overall binding specificity of many proteins is unknown and remains an active area of research. Although existing PWMs are more reliable predictors than consensus string ma...
متن کاملIdentification of the binding sites of regulatory proteins in bacterial genomes.
We present an algorithm that extracts the binding sites (represented by position-specific weight matrices) for many different transcription factors from the regulatory regions of a genome, without the need for delineating groups of coregulated genes. The algorithm uses the fact that many DNA-binding proteins in bacteria bind to a bipartite motif with two short segments more conserved than the i...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2006