• CONREAL

  • Referenced in 2 articles [sw18497]
  • identification and visualization of conserved transcription factor binding sites. The use of orthologous sequences ... identification of conserved transcription factor binding sites (TFBSs), which are characterized by their relatively short...
  • FISim

  • Referenced in 3 articles [sw35291]
  • similarity measure between transcription factor binding sites based on the fuzzy integral. Results: We propose...
  • cosmo

  • Referenced in 3 articles [sw06106]
  • example, represent a common transcription factor binding site. The algorithm is similar to MEME ... knowledge about the structure of the transcription factor in question. The unknown motif width...
  • MotifVoter

  • Referenced in 3 articles [sw35324]
  • generic motif finders. Motivation: Locating transcription factor binding sites (motifs) is a key step...
  • MoTeX

  • Referenced in 3 articles [sw34563]
  • successful in extracting known composite transcription factor binding sites from real datasets. Conclusions...
  • fREDUCE

  • Referenced in 2 articles [sw35521]
  • novel motif predictions for transcription factors with poorly characterized binding sites. Conclusion: We demonstrate that ... prediction of degenerate transcription factor binding sites, especially from array datasets with weak signals that...
  • PeakRanger

  • Referenced in 2 articles [sw12011]
  • handle punctate sites, such as transcriptional factor binding sites, or broad regions, such as histone...
  • CATS

  • Referenced in 1 article [sw35656]
  • based program for identifying clustered transcription factor binding sites. We have developed a program, Cluster ... CATS), which identifies clusters of transcription factor binding sites in any genome sequence. The program ... used for single or multiple transcription factors for which consensus sequences have been deduced based ... CATS for clusters of different transcription factor binding sites may facilitate the identification of genes...
  • KIRMES

  • Referenced in 4 articles [sw35269]
  • problem is the identification of transcription factor (TF) binding sites in promoter regions of potential...
  • ORegAnno

  • Referenced in 2 articles [sw18500]
  • experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release ... over 3853 genes and 465 transcription factors from 19 species. A new feature called ... species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines...
  • TOUCAN

  • Referenced in 2 articles [sw17181]
  • comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules...
  • Chippeakanno

  • Referenced in 2 articles [sw18996]
  • most conserved elements and other transcription factor binding sites supplied by users. Starting...
  • Seeder

  • Referenced in 2 articles [sw35336]
  • Motivation: The computational identification of transcription factor binding sites is a major challenge in bioinformatics...
  • modENCODE

  • Referenced in 2 articles [sw22998]
  • mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure...
  • WaveSeq

  • Referenced in 2 articles [sw22384]
  • various epigenetic phenomena such as, transcription factor binding sites and histone modifications. Histone modification profiles...
  • PMS5

  • Referenced in 2 articles [sw24069]
  • finding transcriptional regulatory elements, transcription factor binding sites, and so on. As a result...
  • ChIP-PaM

  • Referenced in 1 article [sw22385]
  • bound DNAs, especially for locating transcription factor binding sites. However, high cost and high rate ... false discovery of transcription factor binding sites identified from ChIP-Seq data significantly limit ... algorithm, ChIP-PaM, for identifying transcription factor target regions in ChIP-Seq datasets. This algorithm ... from regions enriched by true transcription factor (TF) binding on the basis of ChIP...
  • MONKEY

  • Referenced in 1 article [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...
  • CplexA

  • Referenced in 3 articles [sw32180]
  • multiple, local and distal, DNA binding sites for transcription factors...
  • PePr

  • Referenced in 2 articles [sw34561]
  • identify genome-wide DNA-binding sites for transcription factors (TFs) and histone modifications. There ... PePr) for identifying consistent or differential binding sites in ChIP-Seq experiments with biological replicates...