ArticleBMC bioinformatics2010
RecMotif: a novel fast algorithm for weak motif discovery.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets.BMC bioinformatics · 2018Article
- RefSelect: a reference sequence selection algorithm for planted (l, d) motif search.BMC bioinformatics · 2016Article
- Extracting DNA words based on the sequence features: non-uniform distribution and integrity.Theoretical biology & medical modelling · 2016Article
- Article
- A fast weak motif-finding algorithm based on community detection in graphs.BMC bioinformatics · 2013Article
- PairMotif+: a fast and effective algorithm for de novo motif discovery in DNA sequences.International journal of biological sciences · 2013Article
- Practical guidelines for the comprehensive analysis of ChIP-seq data.PLoS computational biology · 2013Article
- Review of Different Sequence Motif Finding Algorithms.Avicenna journal of medical biotechnologyReview
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Authors and funding
4 authors.
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Abstract
backgroundWeak motif discovery in DNA sequences is an important but unresolved problem in computational biology. Previous algorithms that aimed to solve the problem usually require a large amount of memory or execution time. In this paper, we proposed a fast and memory efficient algorithm, RecMotif, which guarantees to discover all motifs with specific (l, d) settings (where l is the motif length and d is the maximum number of mutations between a motif instance and the true motif).
resultsComparisons with several recently proposed algorithms have shown that RecMotif is more scalable for handling longer and weaker motifs. For instance, it can solve the open challenge cases such as (40, 14) within 5 hours while the other algorithms compared failed due to either longer execution times or shortage of memory space. For real biological sequences, such as E.coli CRP, RecMotif is able to accurately discover the motif instances with (l, d) as (18, 6) in less than 1 second, which is faster than the other algorithms compared.
conclusionsRecMotif is a novel algorithm that requires only a space complexity of O(m²n) (where m is the number of sequences in the data and n is the length of the sequences).
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