• 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...