• Rfam

  • Referenced in 33 articles [sw04637]
  • classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these...
  • REDfly

  • Referenced in 5 articles [sw29315]
  • identification and study of the cis-regulatory elements that control gene expression are important areas ... facilitate large-scale bioinformatics studies of cis-regulation in metazoan species. Drosophila melanogaster, with ... regulatory bioinformatics. We have merged two existing Drosophila resources, the REDfly database of cis-regulatory...
  • GAME

  • Referenced in 4 articles [sw17420]
  • GAME: Detecting cis-regulatory elements using a genetic algorithm. Motivation: Identification of a transcription factor...
  • rVISTA

  • Referenced in 4 articles [sw18501]
  • factor binding site (TFBS) patterns of cis-regulatory elements represents a challenge, but holds promise...
  • INCLUSive

  • Referenced in 4 articles [sw17183]
  • data and the discovery of cis-regulatory sequence elements. The tools allow normalization, filtering...
  • Seeder

  • Referenced in 2 articles [sw35336]
  • fast and reliable prediction of cis-regulatory elements in eukaryotic promoters. The algorithm is tested...
  • SPACER

  • Referenced in 2 articles [sw35520]
  • SPACER: identification of cis-regulatory elements with non-contiguous critical residues. Results: We present...
  • QGRS-H Predictor

  • Referenced in 1 article [sw27631]
  • roles of RNA G-quadruplexes as cis-regulatory elements of post-transcriptional gene expression. Large ... telomeric and gene flanking regions. Identifying conserved regulatory motifs helps validate computations and enhances accuracy ... homologous G-quadruplex forming sequences as cis-regulatory elements in the context...
  • CisGenome

  • Referenced in 1 article [sw31703]
  • tiling array, ChIP-seq, genome and cis-regulatory element analysis...
  • pyDNase

  • Referenced in 1 article [sw17300]
  • eukaryotic genes is regulated by cis-regulatory elements such as promoters and enhancers, which bind...
  • RNAiFold2T

  • Referenced in 0 articles [sw15050]
  • switches. Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon ... thermosensor internal ribosome entry site (thermo-IRES) elements, whose normalized cap-independent transla- tion...
  • R

  • Referenced in 10196 articles [sw00771]
  • R is a language and environment for statistical...
  • NEURON

  • Referenced in 189 articles [sw03059]
  • Parallel network simulations with NEURON. The NEURON simulation...
  • Rnamotif

  • Referenced in 10 articles [sw04638]
  • The rnamotif program [1] searches a database for...
  • LIBSVM

  • Referenced in 1204 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • WEKA

  • Referenced in 306 articles [sw06435]
  • WEKA: Waikato Environment for Knowledge Analysis. WEKA is...
  • Biopython

  • Referenced in 20 articles [sw07357]
  • Biopython: freely available Python tools for computational molecular...
  • minet

  • Referenced in 8 articles [sw08432]
  • minet: A R/Bioconductor Package for Inferring Large Transcriptional...
  • Spikenet

  • Referenced in 12 articles [sw08892]
  • SpikeNET: an event-driven simulation package for modelling...
  • Footprinter

  • Referenced in 9 articles [sw09003]
  • FootPrinter: a program designed for phylogenetic footprinting. Phylogenetic...