• CPMD

  • Referenced in 1 article [sw21890]
  • toolbox for change point and constrained motif discovery. Change Point Discovery (CPD) and Constrained Motif...
  • FastMotif

  • Referenced in 1 article [sw34315]
  • FastMotif: spectral sequence motif discovery . Results: We present FastMotif, a new motif discovery algorithm that ... data. On HT-Selex data, FastMotif extracts motif profiles that match those computed by various...
  • MotifCM

  • Referenced in 1 article [sw09377]
  • analysis. In this paper, a novel motif discovery method based on motif clustering and matching...
  • CMfinder

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

  • Referenced in 1 article [sw28370]
  • Matrix Profile XI: SCRIMP++: Time Series Motif Discovery at Interactive Speeds...
  • DRIMust

  • Referenced in 1 article [sw29654]
  • website http://drimust.technion.ac.il for de novo motif discovery services. The DRIMust algorithm is based ... suffix trees for an efficient enumeration of motif candidates. DRIMust takes as input ranked lists...
  • Cistrome

  • Referenced in 1 article [sw16943]
  • feature association, gene expression analyses, and motif discovery. Cistrome is available at http://cistrome.org/ap/....
  • Nebula

  • Referenced in 1 article [sw16944]
  • immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation of the density...
  • MEME

  • Referenced in 14 articles [sw15711]
  • protein sequence motifs. MEME (Multiple EM for Motif Elicitation) is one of the most widely ... sets of biological sequences. Applications include the discovery of new transcription factor binding sites ... server, users can also access the Motif Alignment and Search Tool to search sequence databases...
  • MADMX

  • Referenced in 6 articles [sw35273]
  • motif. By extracting only maximal dense motifs, madmx reduces the output size and improves performance ... while enhancing the quality of the discoveries. The efficiency of our approach relies ... allows for the construction of maximal dense motifs in a bottom-up fashion, while avoiding...
  • GlobPlot

  • Referenced in 8 articles [sw06213]
  • sequence segments often contain short linear peptide motifs (e.g. SH3-binding sites) which are important ... present here a new tool for discovery of such unstructured, or disordered regions within proteins ... successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that...
  • TFBSTools

  • Referenced in 0 articles [sw18912]
  • provides a wrapper of de novo motif discovery software...
  • Footprinter

  • Referenced in 10 articles [sw09003]
  • Phylogenetic footprinting is a method for the discovery of regulatory elements ... does so by identifying the best conserved motifs in those homologous regions. This note describes...
  • MotifMiner

  • Referenced in 7 articles [sw35523]
  • Traditionally, researchers have identified these patterns, or motifs, manually using biochemical expertise. However, with ... structural patterns in molecules. Previous automated substructure discovery approaches have each introduced variations of similar ... general toolkit for automatically identifying common motifs in most any scientific molecular dataset. We describe...
  • jmotif

  • Referenced in 1 article [sw15368]
  • time series motif (i.e., recurrent pattern), discord (i.e., anomaly), and characteristic pattern discovery along with...
  • FIMO

  • Referenced in 6 articles [sw17298]
  • scanning DNA or protein sequences with motifs described as position-specific scoring matrices. The program ... value and then applies false discovery rate analysis to estimate a q-value for each...
  • MPBind

  • Referenced in 1 article [sw34401]
  • MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX ... specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro, rather ... making them well-suited for high-throughput discovery. However, a large fraction of the most ... activity. Here, we present MPBind, a Meta-motif-based statistical framework and pipeline to Predict...
  • MEME-LaB

  • Referenced in 1 article [sw23004]
  • MEME-LaB: motif analysis in clusters. SUMMARY: Genome-wide expression analysis can result in large ... Although there are tools for ab initio discovery of transcription factor-binding sites, most ... tool wraps MEME (an ab initio motif finder), providing an interface for users to input...
  • CyclinPred

  • Referenced in 1 article [sw22405]
  • sequences with low sequence similarity making discovery of novel cyclins and establishing orthologous relationships amongst ... difficult task. The currently identified cyclin motifs and cyclin associated domains do not represent...
  • SegHMC

  • Referenced in 1 article [sw20932]
  • discovery of cis-regulatory module) for the discovery of cis-regulatory module based on segmental ... combination of a group of motifs but also further introduces the frequency of the occurrence...