• JASPAR

  • Referenced in 40 articles [sw18502]
  • detection of potential transcription factor binding sites. The preferred models for representation of transcription factor ... annotated, high‐quality, matrix‐based transcription factor binding site profiles for multicellular eukaryotes. The profiles ... nucleotide sequences experimentally demonstrated to bind transcription factors. The database is complemented...
  • TRANSFAC

  • Referenced in 73 articles [sw17201]
  • database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/ ... well as by data on plant sites and factors. Moreover, TRANSFAC has been extended ... relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features ... scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about...
  • MEME

  • Referenced in 14 articles [sw15711]
  • include the discovery of new transcription factor binding sites and protein domains. MEME works...
  • TileMap

  • Referenced in 13 articles [sw35530]
  • survey genomic transcriptional activities and transcription factor binding sites at high resolution. The goal ... tools to identify genomic loci that show transcriptional or protein binding patterns of interest. Results...
  • MATCH

  • Referenced in 6 articles [sw23010]
  • MATCH: A tool for searching transcription factor binding sites in DNA sequences. Match ... based tool for searching putative transcription factor binding sites in DNA sequences. Match is closely ... great variety of different transcription factor binding sites. Several sets of optimised matrix...
  • PhyME

  • Referenced in 10 articles [sw35645]
  • addresses the problem of discovering transcription factor binding sites in heterogeneous sequence data, which includes...
  • REDfly

  • Referenced in 5 articles [sw29315]
  • regulatory modules and transcription factor binding sites in Drosophila. The identification and study ... long history of experimental studies of transcriptional regulation, represents the ideal system for regulatory bioinformatics ... FlyReg database of transcription factor binding sites (TFBSs), into a single integrated database containing extensive ... regulatory modules and their constituent binding sites. With the enhanced functionality made possible through this...
  • BayesPeak

  • Referenced in 7 articles [sw18843]
  • find the locations of transcription factor binding sites, modified histones or nucleosomes. The BayesPeak algorithm...
  • FindPeaks

  • Referenced in 7 articles [sw29575]
  • areas of gene enrichment and transcription factor binding site locations, as well as for estimating...
  • DWE

  • Referenced in 3 articles [sw29590]
  • Word Enumerator. Motivation: Tissue-specific transcription factor binding sites give insight into tissue-specific transcription ... novo tissue-specific transcription factor binding site discovery using expression information in addition to sequence ... statistical approach to find overrepresented transcription factor binding sites in a foreground promoter sequence ... approach naturally extends to synergistic transcription factor binding site search. We find putative transcription factor...
  • Babelomics

  • Referenced in 6 articles [sw36144]
  • Prot keywords, analysis of predicted transcription factor binding sites, chromosomal positions and presence in tissues ... assignment and transference of information), FatiWise, transcription factor association test, GenomeGO and tissues mining tool...
  • CONFAC

  • Referenced in 4 articles [sw35535]
  • Here we describe the conserved transcription factor binding site (CONFAC) software that enables the high ... throughput identification of conserved transcription factor binding sites (TFBSs) in the regulatory regions of hundreds...
  • MatInspector

  • Referenced in 6 articles [sw21812]
  • library of matrix descriptions for transcription factor binding sites to locate matches in DNA sequences...
  • Expression Profiler

  • Referenced in 6 articles [sw08351]
  • promoter sequences for predicting transcription factor binding sites. Several clustering analysis method implementations and tools...
  • rVISTA

  • Referenced in 3 articles [sw18501]
  • rVISTA 2.0: evolutionary analysis of transcription factor binding sites. dentifying and characterizing the transcription factor ... regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory...
  • F-Seq

  • Referenced in 5 articles [sw17297]
  • specific sequence features, such as transcription factor binding sites (ChIP-seq) or regions of open...
  • GAME

  • Referenced in 4 articles [sw17420]
  • algorithm. Motivation: Identification of a transcription factor binding sites is an important aspect...
  • WordSpy

  • Referenced in 5 articles [sw19955]
  • dictionary and learning a grammar. Transcription factor (TF) binding sites or motifs (TFBMs) are functional ... that play an essential role in gene transcriptional regulation. Although many experimental and computational methods...
  • COMODE

  • Referenced in 3 articles [sw36145]
  • sequences. Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary ... MEME, Gibbs motif sampler) model binding sites as families of sequences described by a position ... address supervising the search for DNA binding sites using the information derived from structural characteristics ... data. Some of the transcription factor binding data of Lee et al. (2002) were also...
  • MONKEY

  • Referenced in 2 articles [sw33139]
  • conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model ... method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic...