• BioProspector

  • Referenced in 29 articles [sw09375]
  • motifs with palindromic patterns, which are prevalent motif patterns in prokaryotes. All these modifications greatly ... showing preliminary success in finding the binding motifs for S. cerevisiae RAP1, B. subtilis...
  • RSIR

  • Referenced in 16 articles [sw26716]
  • discovery. MOTIVATION: Identification of transcription factor binding motifs (TFBMs) is a crucial first step towards...
  • WoLF PSORT

  • Referenced in 11 articles [sw27721]
  • functional motifs such as DNA-binding motifs. After conversion, a simple k-nearest neighbor classifier...
  • STAMP

  • Referenced in 6 articles [sw17264]
  • tool for exploring DNA-binding motif similarities. STAMP is a newly developed web server that ... support the study of DNA-binding motifs. STAMP may be used to query motifs against ... with newly discovered motifs. STAMP also automatically builds multiple alignments, familial binding profiles and similarity ... known binding sites. STAMP also directly accepts the output files from 12 supported motif-finders...
  • WordSpy

  • Referenced in 5 articles [sw19955]
  • WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar. Transcription ... factor (TF) binding sites or motifs (TFBMs) are functional cis-regulatory DNA sequences that play ... regulatory sequences with motif binding sites highlighted. The web server of WordSpy is available...
  • DREME

  • Referenced in 3 articles [sw17299]
  • find the short, core DNA-binding motifs of eukaryotic TFs, and optimized to analyze very ... minutes. Using DREME, we discover the binding motifs of the the ChIP ... Esrrb, we discover the binding motifs for eight cofactor TFs important in the maintenance ... same dataset. DREME can also perform discriminative motif discovery, and we use this feature...
  • GAME

  • Referenced in 4 articles [sw17420]
  • novo discovery of a binding motif (collection of binding sites). Recently, a scoring function formulation ... that allows for the comparison of discovered motifs from different programs [S.T. Jensen...
  • HPeak

  • Referenced in 4 articles [sw29576]
  • prevalence of the expected transcription factor binding motifs in ChIP-enriched sequences relative ... along with improved sensitivity and specificity of binding site detection. Additional file and the HPeak...
  • PlantTFDB

  • Referenced in 4 articles [sw17023]
  • expression information, expert-curated functional description, binding motifs, regulation information, interaction, references, and cross-linsk...
  • MotifVoter

  • Referenced in 3 articles [sw35324]
  • motif finders. Motivation: Locating transcription factor binding sites (motifs) is a key step in understanding ... ensemble method, MotifVoter, to predict the motifs and binding sites. Evaluations on 186 datasets show ... than 95% of the binding sites found by its component motif finders. In terms...
  • CisModule

  • Referenced in 5 articles [sw35646]
  • encoded in cis-regulatory modules. The binding sites for a set of interacting transcription factors ... same modules. Current de novo motif discovery methods do not take advantage of this knowledge ... also more sensitive in detecting motif patterns and binding sites than standard motif discovery methods...
  • PICS

  • Referenced in 3 articles [sw37329]
  • were more consistent with computationally predicted binding motifs than the alternative methods MACS, QuEST, CisGenome...
  • NestedMICA

  • Referenced in 4 articles [sw35335]
  • finder originally developed for finding transcription binding site motifs, to find short protein signals...
  • COMODE

  • Referenced in 3 articles [sw36145]
  • sequences. Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary ... used methods (e.g., MEME, Gibbs motif sampler) model binding sites as families of sequences described ... address supervising the search for DNA binding sites using the information derived from structural characteristics ... profiles or on specific parameters of the motif PWMs. The parameters of this extended model...
  • fREDUCE

  • Referenced in 2 articles [sw35521]
  • detection of weak or degenerate binding motifs from gene expression or ChIP-chip data. fREDUCE ... make novel motif predictions for transcription factors with poorly characterized binding sites. Conclusion: We demonstrate ... binding sites, especially from array datasets with weak signals that may elude other motif detection...
  • GlobPlot

  • Referenced in 7 articles [sw06213]
  • often contain short linear peptide motifs (e.g. SH3-binding sites) which are important for protein ... successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that...
  • BioOptimizer

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

  • Referenced in 3 articles [sw35291]
  • binding affinity. FISim provides excellent results when dealing with sets of randomly generated motifs ... measure to successfully identify motifs that describe binding sites for the same ... study the reliability of fuzzy technology for motif comparison tasks is proven...
  • ATtRACT

  • Referenced in 1 article [sw29373]
  • binding proteins and associated motifs. RNA-binding proteins (RBPs) play a crucial role ... resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this ... RBPs and 1583 RBP consensus binding motifs, 192 of which are not present...
  • motifDiverge

  • Referenced in 1 article [sw24160]
  • assessing the statistical significance of gene regulatory motif divergence between two DNA sequences. Next-generation ... sequences differ in their number of binding site motifs for a given transcription factor ... protein. Binding site motifs impart regulatory function by providing TFs the opportunity to bind ... species; but despite the importance of TF motifs for gene expression, no method exists...