Proceedings ArticleDOI
A Simple Algorithm for (l, d) Motif Search1
Dolly Sharma,Sanguthevar Rajasekaran +1 more
- pp 148-154
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TLDR
The algorithm proposed here is an extension of PMS3 and uses a very simple approach and solves challenging instances ((21, 8), for example) that have not been reported solved before in the literature.Abstract:
Extracting meaningful patterns from voluminous amount of biological data is a very big challenge. Motifs are biological patterns of great interest to biologists. There are different versions of the Motif Finding Problem. In this paper we concentrate on the Planted (l, d) Motif Search Problem. There have been numerous algorithms designed to solve this problem. Many instances of the Planted (l, d) Motif Problem have been identified as challenging instances. The algorithm proposed here is an extension of PMS3 [1]. It uses a very simple approach and solves challenging instances ((21, 8), for example) that have not been reported solved before in the literature. We also propose a new algorithm PMS3p. We expect PMS3p to be significantly faster than PMS3.read more
Citations
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Journal ArticleDOI
Improved exact enumerative algorithms for the planted (l, d)-motif search problem
TL;DR: Efficient exact algorithms based on the previous algorithms called qPMSPruneI and qPMS7 that traverse a search tree starting from a l-length substring of an input string are proposed and it will be shown that the proposed algorithms outperform thePrevious algorithms.
Journal Article
Review of Different Sequence Motif Finding Algorithms.
TL;DR: A general classification of motif discovery algorithms with new sub-categories that facilitate building a successful motif discovery algorithm is presented and a summary of comparison between them is presented.
Journal ArticleDOI
WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures.
Jens Lichtenberg,Kyle Kurz,Xiaoyu Liang,Rami Al-Ouran,Lev Neiman,L Nau,Joshua D. Welch,Edwin Jacox,Thomas Bitterman,Klaus Ecker,Laura Elnitski,Frank Drews,Stephen S. Lee,Lonnie R. Welch +13 more
TL;DR: WordSeeker effectively utilizes concurrent computing platforms to enable the identification of putative functional elements in genomic data sets and facilitates the analysis of the large quantity of sequenced genomic data.
Proceedings ArticleDOI
Reconstructing phylogenetic network with ReTF algorithm (rearranging transcriptional factor)
Shamita Malik,Dolly Sharma +1 more
TL;DR: The idea behind ReTF is rearranging the input sequences in a way that the new arrangement gives a better tree, since the order of input sequences affects the outcomes of phylogenetic network.
References
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Proceedings Article
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Pavel A. Pevzner,Sing-Hoi Sze +1 more
TL;DR: This work complements existing statistical and machine learning approaches to this problem by a combinatorial approach that proved to be successful in identifying very subtle signals in DNA sequences.
Journal ArticleDOI
Finding motifs using random projections.
Jeremy Buhler,Martin Tompa +1 more
TL;DR: A novel motif-discovery algorithm, PROJECTION, is introduced, designed to enhance the performance of existing motif finders using random projections of the input's substrings, and is robust to nonuniform background sequence distributions and scales to larger amounts of sequence than that specified in the original challenge.
Proceedings ArticleDOI
Finding motifs using random projections
Jeremy Buhler,Martin Tompa +1 more
TL;DR: A novel motif discovery algorithm based on the use of random projections of the input's substrings is introduced that performs better than existing algorithms and typically solves the difficult (14,4)-, (16,5)-, and (18,6)-motif problems quite efficiently.
Journal ArticleDOI
Finding composite regulatory patterns in DNA sequences
Eleazar Eskin,Pavel A. Pevzner +1 more
TL;DR: This paper presents a MITRA (MIsmatch TRee Algorithm) approach for discovering composite signals and demonstrates that MITRA performs well for both monad and composite patterns by presenting experiments over biological and synthetic data.
Journal ArticleDOI
On the closest string and substring problems
Ming Li,Bin Ma,Lusheng Wang +2 more
TL;DR: Two polynomial-time approximationalgorithms with approximation ratio 1 + ε for any smallε to settle both the Closest String problem and the ClOSest Substring problem are presented.