• BioProspector

  • Referenced in 29 articles [sw09375]
  • motifs with palindromic patterns, which are prevalent motif patterns in prokaryotes. All these modifications greatly ... Besides showing preliminary success in finding the binding motifs for S. cerevisiae RAP1, B. subtilis ... have used BioProspector to find s54 motif from M. xanthus genome, many B. subtilis motifs...
  • Kavosh

  • Referenced in 12 articles [sw29733]
  • Kavosh: a new algorithm for finding network motifs. Background: Complex networks are studied across many ... complex networks. Existing algorithms for finding network motifs are extremely costly in CPU time ... obtained results with three well-known motif finding tools. For comparison, the CPU time, memory ... Besides, Kavosh can be employed for finding motifs of size greater than eight, while most...
  • MotifCut

  • Referenced in 8 articles [sw35400]
  • MotifCut: regulatory motifs finding with maximum density subgraphs. Results: We present MotifCut, a graph-theoretic ... approach to motif finding leading to a convex optimization problem with a polynomial time solution ... this graph, we search for a motif as the maximum density subgraph, which ... both synthetic and real yeast motifs, and find that it compares favorably to existing popular...
  • BioOptimizer

  • Referenced in 6 articles [sw17421]
  • expensive and time-consuming. Many motif-finding programs have been developed, but no program ... situations. Practitioners often find it difficult to judge which of the motifs predicted by these ... motif signal found by any motif-finding program. The accuracy of BioOptimizer, which ... superior to using any of these motif-finding programs alone when evaluated by both simulation...
  • PhyME

  • Referenced in 9 articles [sw35645]
  • PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. Background: This paper...
  • WordSpy

  • Referenced in 5 articles [sw19955]
  • grammar. Transcription factor (TF) binding sites or motifs (TFBMs) are functional cis-regulatory DNA sequences ... experimental and computational methods have been developed, finding TFBMs remains a challenging problem. We propose ... develop a novel dictionary based motif finding algorithm, which we call WordSpy. One significant feature ... algorithm is suitable for genome-wide motif finding; it is capable of discovering hundreds...
  • GAME

  • Referenced in 4 articles [sw17420]
  • used in conjunction with other motif-finding software. Results: We introduce software, GAME, which utilizes ... genetic algorithm to find optimal motifs in DNA sequences. GAME evolves motifs with high fitness ... which eliminate the reliance on additional motif-finding programs. In addition to using standard genetic ... additional operators that are specific to the motif discovery problem. We demonstrate the superior performance...
  • CMfinder

  • Referenced in 6 articles [sw17265]
  • CMfinder – A covariance model based RNA motif finding algorithm. Motivation: The recent discoveries of large ... quality identification and characterization of conserved RNA motifs that can be readily used for database...
  • KIRMES

  • Referenced in 4 articles [sw35269]
  • that combines the benefits of existing motif finding with the ones of support vector machines ... SVMs) to find degenerate motifs in order to improve the modeling of regulatory modules...
  • NestedMICA

  • Referenced in 4 articles [sw35335]
  • developed for finding transcription binding site motifs, to find short protein signals, and compared...
  • FIMO

  • Referenced in 6 articles [sw17298]
  • specific frequency matrix. Results: We describe Find Individual Motif Occurrences (FIMO), a software tool...
  • GeneMarkS

  • Referenced in 6 articles [sw23024]
  • starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Improving the accuracy ... uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models of coding ... upstream to a gene start. Therefore, sequence motifs related to transcription and translation regulatory sites...
  • MOPAC

  • Referenced in 2 articles [sw02841]
  • MOPAC: motif finding by preprocessing and agglomerative clustering from microarrays. We propose a novel strategy ... genes. Our interest is to find common regulatory motifs that are responsible for the upregulation ... time. Our objective is to find the common motifs that are present in at least ... propose a new algorithm for finding such motifs through stages of pre-processing, de-noising...
  • PMS5

  • Referenced in 2 articles [sw24069]
  • exact algorithm for the (ℓ, d)-motif finding problem. BACKGROUND: Motifs are patterns found ... drug design, etc. They are helpful in finding transcriptional regulatory elements, transcription factor binding sites ... result, the problem of identifying motifs is very crucial in biology. RESULTS: Many facets ... that always finds all the (ℓ, d)-motifs on a given input set is called...
  • MODA

  • Referenced in 5 articles [sw29734]
  • computationally hard problem and finding rather large motifs (larger than 8 nodes) by means...
  • DREME

  • Referenced in 3 articles [sw17299]
  • present DREME, a motif discovery algorithm specifically designed to find the short, core DNA-binding ... Esrrb, we discover the binding motifs for eight cofactor TFs important in the maintenance ... other commonly used algorithms find at most two cofactor motifs in this same dataset. DREME ... scales linearly in dataset size, finds multiple, non-redundant motifs and reports a reliable measure...
  • FR3D

  • Referenced in 6 articles [sw13838]
  • Fred”. It was developed to find small RNA motifs (two to 20 nucleotides...
  • MUSA

  • Referenced in 2 articles [sw35518]
  • propose a new algorithm, MUSA (Motif finding using an UnSupervised Approach), that can be used ... either to autonomously find over-represented complex motifs or to estimate search parameters for modern...
  • MotifClick

  • Referenced in 2 articles [sw29728]
  • developed to find a set of cis-regulatory binding sites called a motif ... different from their background sequences. However, some motifs may have a similar nucleotide distribution ... that of their background sequences. To find binding sites with length k, we construct ... eukaryotes, MotifClick outperforms existing leading motif-finding tools for prediction accuracy and balancing the prediction...
  • fREDUCE

  • Referenced in 2 articles [sw35521]
  • REDUCE as well as other known motif-finding programs. We have also used fREDUCE...