• RSIR

  • Referenced in 15 articles [sw26716]
  • RSIR: regularized sliced inverse regression for motif discovery. MOTIVATION: Identification of transcription factor binding motifs...
  • TEIRESIAS

  • Referenced in 15 articles [sw35978]
  • sequences: The TEIRESIAS algorithm. MOTIVATION: The discovery of motifs in biological sequences is an important ... algorithm for the discovery of rigid patterns (motifs) in biological sequences. Our method is combinatorial ... validate the approach through the discovery of previously reported patterns; (ii) demonstrate the capability...
  • PhyME

  • Referenced in 10 articles [sw35645]
  • demonstrate that the new approach improves motif discovery by exploiting multiple species information...
  • CisModule

  • Referenced in 6 articles [sw35646]
  • hierachical mixture modeling. CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling ... same modules. Current de novo motif discovery methods do not take advantage of this knowledge ... model, a new de novo motif-module discovery algorithm, CisModule, is developed for the Bayesian ... patterns and binding sites than standard motif discovery methods...
  • WebMOTIFS

  • Referenced in 4 articles [sw35522]
  • have shown that the accuracy of motif discovery can be significantly improved by using multiple ... novo motif discovery programs and using randomized control calculations to identify the most significant motifs ... submission form, users can run several motif discovery programs and score, cluster and visualize ... results. In addition, the Bayesian motif discovery program THEME can be used to determine...
  • MODA

  • Referenced in 4 articles [sw29734]
  • MODA: an efficient algorithm for network motif discovery in biological networks. In recent years, interest ... developed in studying local features named motifs ... building blocks of networks. Unfortunately, network motif discovery is a computationally hard problem and finding ... current state-of-the-art motif discovery algorithms. While most of the algorithms rely...
  • DREME

  • Referenced in 3 articles [sw17299]
  • Bailey TL (2011) DREME: motif discovery in transcription factor ChIP-seq data. Motivation: Transcription factor ... provide unique challenges and opportunities for motif discovery. Most existing motif discovery algorithms ... Results: We present DREME, a motif discovery algorithm specifically designed to find the short, core ... dataset. DREME can also perform discriminative motif discovery, and we use this feature to provide...
  • BioOptimizer

  • Referenced in 6 articles [sw17421]
  • Bayesian scoring function approach to motif discovery. Motivation: Transcription factors (TFs) bind directly to short ... sites is expensive and time-consuming. Many motif-finding programs have been developed...
  • NestedMICA

  • Referenced in 4 articles [sw35335]
  • NestedMICA as an ab initio protein motif discovery tool. Background: Discovering overrepresented patterns in amino ... adapted and extended NestedMICA, an ab initio motif finder originally developed for finding transcription binding ... MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven ... parts of sequences that do not contain motifs of interest. In order to assess NestedMICA...
  • STAMP

  • Referenced in 5 articles [sw17264]
  • motif-finders, enabling quick interpretation of motif-discovery analyses. STAMP is available at http://www.benoslab.pitt.edu...
  • GAME

  • Referenced in 4 articles [sw17420]
  • developed for the de novo discovery of a binding motif (collection of binding sites). Recently ... operators that are specific to the motif discovery problem. We demonstrate the superior performance ... GAME algorithm that allows the motif width to be unknown. Availability:http://mail.med.upenn.edu/ zhiwei/GAME...
  • Varun

  • Referenced in 4 articles [sw13191]
  • Extensible Motifs under Saturation Constraints. The discovery of motifs in biosequences is frequently torn between ... Varun¹ is described, implementing the discovery of extensible motifs of the type considered. The merits...
  • NeMoFinder

  • Referenced in 4 articles [sw29732]
  • vast interactomes.We describe an efficient network motif discovery algorithm, NeMoFinder, that can mine meso-scale...
  • ParaMEME

  • Referenced in 4 articles [sw29726]
  • interface for a DNA and protein motif discovery tool. Many advanced software tools fail ... such program, MEME, discovers repeated patterns, called motifs, in sets of DNA or protein sequences...
  • Seeder

  • Referenced in 2 articles [sw35336]
  • Seeder: discriminative seeding DNA motif discovery. Motivation: The computational identification of transcription factor binding sites ... novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction ... perform equally or better than other motif discovery tools. The algorithm is applied...
  • TSMining

  • Referenced in 1 article [sw29030]
  • implementation of SAX transformation, univariate motif discovery (based on the random projection method), multivariate motif ... Details on univariate motif discovery method implemented can be found in B. Chiu, E. Keogh ... Lonardi, Probabilistic discovery of time series motifs, ACM SIGKDD, Washington ... Details on the multivariate motif discovery method implemented can be found in A. Vahdatpour...
  • Tmod

  • Referenced in 1 article [sw20498]
  • Tmod: toolbox of motif discovery. Summary: Motif discovery is an important topic in computational transcriptional ... field and many de novo motif-finding tools have been developed, each may have ... present a software called Toolbox of Motif Discovery (Tmod) for Windows operating systems. The current ... Tmod integrates 12 widely used motif discovery programs: MDscan, BioProspector, AlignACE, Gibbs Motif Sampler, MEME...
  • PMS6MC

  • Referenced in 1 article [sw28061]
  • PMS6MC: a multicore algorithm for motif discovery. We develop an efficient multicore algorithm, PMS6MC ... motif discovery problem in which we are to find all strings of length l that ... fastest single-core algorithm for motif discovery in large instances. The speedup, relative to PMS6 ... times faster than other parallel algorithms for motif search on large instances...
  • DECOD

  • Referenced in 1 article [sw33137]
  • accurate discriminative DNA motif finding. Motivation: Motif discovery is now routinely used in high-throughput ... challenges. The first is speed. Many motif discovery methods do not scale well to large ... issue is identifying discriminative rather than generative motifs. Such discriminative motifs are important for identifying ... developed a method for DECOnvolved Discriminative motif discovery (DECOD). DECOD uses a k-mer count...
  • RecMotif

  • Referenced in 1 article [sw35236]
  • novel fast algorithm for weak motif discovery. Background: Weak motif discovery in DNA sequences ... algorithm, RecMotif, which guarantees to discover all motifs with specific (l, d) settings (where...