• BioProspector

  • Referenced in 29 articles [sw09375]
  • BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. The development ... BioProspector, a C program using a Gibbs sampling strategy, examines the upstream region of genes ... pattern group and looks for regulatory sequence motifs. BioProspector uses Markov background to model...
  • KIRMES

  • Referenced in 4 articles [sw35269]
  • position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed ... algorithm that combines the benefits of existing motif finding with the ones of support vector...
  • NestedMICA

  • Referenced in 4 articles [sw35335]
  • finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven ... Monte Carlo technique called Nested Sampling. It uses multi-class sequence background models to represent ... parts of sequences that do not contain motifs of interest. In order to assess NestedMICA...
  • Prnam-PC

  • Referenced in 19 articles [sw22422]
  • uncharacterized RNA sequence containing many GAC motifs, which of them can be methylated, and which ... called pRNAm-PC, in which RNA sequence samples are expressed by a novel mode...
  • ARGO

  • Referenced in 2 articles [sw35519]
  • ARGO_Motifs program. Analysis and recognition of tissue-specific promoters in five gene samples demonstrated...
  • GeneMarkS

  • Referenced in 6 articles [sw23024]
  • microbial genomes. Implications for finding sequence motifs in regulatory regions. Improving the accuracy of prediction ... coding regions and the Gibbs sampling multiple alignment program. GeneMarkS predicted precisely ... upstream to a gene start. Therefore, sequence motifs related to transcription and translation regulatory sites...
  • SeedHam

  • Referenced in 1 article [sw33130]
  • categorical distribution from a (non-uniform) Hamming sample. The SeedHam method is intended ... hundreds of Mbases) containing enriched motif instances. A variant of the method is introduced that...
  • Methylation

  • Referenced in 1 article [sw29653]
  • positions and subjects (cancer and healthy samples). Importantly, our approach, especially the use of attention ... information. We demonstrate this by linking several motifs and genes to methylation activity, including Nodal...
  • FASTAptamer

  • Referenced in 1 article [sw28242]
  • selection and searches for degenerate sequence motifs. While originally designed for aptamer selections, FASTAptamer ... peptide, antibody fragment, mRNA, etc.). FASTAptamer software, sample data and a user’s guide...
  • PePr

  • Referenced in 1 article [sw34561]
  • read counts across the genome among biological samples with a negative binomial distribution and uses ... consistent regions with enriched read counts, high motif occurrence rate and known characteristics...
  • MATCONT

  • Referenced in 363 articles [sw00551]
  • MATCONT: Matlab software for bifurcation study of dynamical...
  • Matlab

  • Referenced in 12074 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • mclust

  • Referenced in 257 articles [sw00563]
  • R package mclust: Normal Mixture Modeling for Model...
  • MiniSat

  • Referenced in 531 articles [sw00577]
  • An extensible SAT-solver. MiniSat is a minimalistic...
  • R

  • Referenced in 8359 articles [sw00771]
  • R is a language and environment for statistical...
  • CUDA

  • Referenced in 1185 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...
  • UCI-ml

  • Referenced in 3041 articles [sw04074]
  • UC Irvine Machine Learning Repository. We currently maintain...
  • Bioconductor

  • Referenced in 298 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • ARPACK

  • Referenced in 783 articles [sw04218]
  • ARPACK is a collection of Fortran77 subroutines designed...