ArticlePloS one2012
qPMS7: a fast algorithm for finding (ℓ, d)-motifs in DNA and protein sequences.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A Review on Planted (Sensors (Basel, Switzerland) · 2022Review
- Freezing firefly algorithm for efficient planted (ℓ, d) motif search.Medical & biological engineering & computing · 2022Article
- A Clustering Approach for Motif Discovery in ChIP-Seq Dataset.Entropy (Basel, Switzerland) · 2019Article
- SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets.BMC bioinformatics · 2018Article
- Exhaustive search of linear information encoding protein-peptide recognition.PLoS computational biology · 2017Article
- RefSelect: a reference sequence selection algorithm for planted (l, d) motif search.BMC bioinformatics · 2016Article
- Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- qPMS9: an efficient algorithm for quorum Planted Motif Search.Scientific reports · 2015Article
- An Affinity Propagation-Based DNA Motif Discovery Algorithm.BioMed research international · 2015Article
- Characterization of human chromosomal material exchange with regard to the chromosome translocations using next-generation sequencing data.Genome biology and evolution · 2014Article
- A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons.Genome biology and evolution · 2014Article
- Efficient sequential and parallel algorithms for planted motif search.BMC bioinformatics · 2014Article
- Article
- PairMotif+: a fast and effective algorithm for de novo motif discovery in DNA sequences.International journal of biological sciences · 2013Article
- PMS: a panoptic motif search tool.PloS one · 2013Article
- Review of Different Sequence Motif Finding Algorithms.Avicenna journal of medical biotechnologyReview
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Detection of rare events happening in a set of DNA/protein sequences could lead to new biological discoveries. One kind of such rare events is the presence of patterns called motifs in DNA/protein sequences. Finding motifs is a challenging problem since the general version of motif search has been proven to be intractable. Motifs discovery is an important problem in biology. For example, it is useful in the detection of transcription factor binding sites and transcriptional regulatory elements that are very crucial in understanding gene function, human disease, drug design, etc. Many versions of the motif search problem have been proposed in the literature. One such is the (ℓ, d)-motif search (or Planted Motif Search (PMS)). A generalized version of the PMS problem, namely, Quorum Planted Motif Search (qPMS), is shown to accurately model motifs in real data. However, solving the qPMS problem is an extremely difficult task because a special case of it, the PMS Problem, is already NP-hard, which means that any algorithm solving it can be expected to take exponential time in the worse case scenario. In this paper, we propose a novel algorithm named qPMS7 that tackles the qPMS problem on real data as well as challenging instances. Experimental results show that our Algorithm qPMS7 is on an average 5 times faster than the state-of-art algorithm. The executable program of Algorithm qPMS7 is freely available on the web at http://pms.engr.uconn.edu/downloads/qPMS7.zip. Our online motif discovery tools that use Algorithm qPMS7 are freely available at http://pms.engr.uconn.edu or http://motifsearch.com.
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