An Entropy-Based Position Projection Algorithm for Motif Discovery
نویسندگان
چکیده
منابع مشابه
An Entropy-Based Position Projection Algorithm for Motif Discovery
Motif discovery problem is crucial for understanding the structure and function of gene expression. Over the past decades, many attempts using consensus and probability training model for motif finding are successful. However, the most existing motif discovery algorithms are still time-consuming or easily trapped in a local optimum. To overcome these shortcomings, in this paper, we propose an e...
متن کاملNeighbourhood Thresholding for Projection-Based Motif Discovery
The PROJECTION algorithm by Buhler and Tompa is one of the best existing methods for solving hard motif discovery problems for monad motifs of fixed length l. In this paper we introduce the AGGREGATION algorithm, which like PROJECTION projects all l-mers from the given input sequences into buckets, but uses a different scheme for selecting buckets for subsequent refinement search. This new neig...
متن کاملAn Efficient Algorithm for String Motif Discovery
Finding common patterns, motifs, in a set of DNA sequences is an important problem in bioinformatics. One common representation of motifs is a string with symbols A, C, G, T and N where N stands for the wildcard symbol. In this paper, we introduce a more general motif discovery problem without any weaknesses of the Planted (l,d)-Motif Problem and also a set of control sequences as an additional...
متن کاملPOWRS: Position-Sensitive Motif Discovery
UNLABELLED Transcription factors and the short, often degenerate DNA sequences they recognize are central regulators of gene expression, but their regulatory code is challenging to dissect experimentally. Thus, computational approaches have long been used to identify putative regulatory elements from the patterns in promoter sequences. Here we present a new algorithm "POWRS" (POsition-sensitive...
متن کاملAn Affinity Propagation-Based DNA Motif Discovery Algorithm
The planted (l, d) motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which f...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: BioMed Research International
سال: 2016
ISSN: 2314-6133,2314-6141
DOI: 10.1155/2016/9127474