• BioProspector

  • Referenced in 29 articles [sw09375]
  • bases, which greatly improved the specificity of the reported motifs. The parameters of the Markov ... whole genome sequences. A new motif scoring function is adopted to allow each input sequences...
  • HPAM

  • Referenced in 3 articles [sw10931]
  • uncertainty of its motif, which allows sites with low specificity (i.e., differing from the best ... alignment or consensus) to still be functional. HPAM is available for public...
  • RNAfbinv

  • Referenced in 1 article [sw17115]
  • based design approach, specific RNA structural motifs with known biological functions are strictly enforced while...
  • FIMO

  • Referenced in 6 articles [sw17298]
  • protein sequence that contributes to the biological function of the sequence in which it resides ... searching with sequence motifs. Critical to nearly any motif-based sequence analysis pipeline ... occurrences of a given motif described by a position-specific frequency matrix. Results: We describe...
  • ARGO

  • Referenced in 2 articles [sw35519]
  • system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters. Reliable ... structural–functional organization of the eukaryotic promoters essential for their function and recognition. However ... specific promoter groups increases the accuracy of promoter recognition and prediction of specific expression features ... queried genes. The ARGO_Motifs package was developed for the detection of sets of region...
  • MI-Sim

  • Referenced in 1 article [sw17108]
  • software includes seven ecological interaction motifs and seven growth function models. Unlike other system analysis ... simple and user-friendly tool specific to ecological population type models, allowing for rapid assessment...
  • PatSearch

  • Referenced in 3 articles [sw17167]
  • detection of patterns and structural motifs in nucleotide sequences. Regulation of gene expression at transcriptional ... comparative analysis as well as to target functional characterization experiments. We present here PatSearch ... fast pattern matcher able to search for specific combinations of oligonucleotide consensus sequences, secondary structure...
  • GAME

  • Referenced in 4 articles [sw17420]
  • improved discovered motifs by optimizing a scoring function. However, BioOptimizer is a very simple algorithm ... discovered motif and so BioOptimizer can only be used in conjunction with other motif-finding ... algorithm to find optimal motifs in DNA sequences. GAME evolves motifs with high fitness from ... randomly generated starting motifs, which eliminate the reliance on additional motif-finding programs. In addition...
  • Cistrome

  • Referenced in 1 article [sw16943]
  • standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three ... genome feature association, gene expression analyses, and motif discovery. Cistrome is available at http://cistrome.org...
  • HubAlign

  • Referenced in 3 articles [sw34150]
  • networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed ... heuristic algorithm to estimate the topological and functional importance of a protein from the global...
  • KeBABS

  • Referenced in 1 article [sw15427]
  • motif kernel. Apart from an efficient implementation of standard position-independent functionality, the kernels ... included as special cases. An annotation-specific variant of the kernels uses annotation information placed...
  • CyclinPred

  • Referenced in 1 article [sw22405]
  • based method for predicting cyclin protein sequences. Functional annotation of protein sequences with low similarity ... difficult task. The currently identified cyclin motifs and cyclin associated domains do not represent ... structure composition and PSI-BLAST generated Position Specific Scoring Matrix (PSSM) profiles. Results obtained from...
  • SPINE-D

  • Referenced in 1 article [sw16912]
  • test set. With greater than 85% overall specificity for detecting residues in both short ... examined for prediction of functional molecular recognition motifs in several case studies. The server...
  • Matlab

  • Referenced in 13100 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • mclust

  • Referenced in 281 articles [sw00563]
  • R package mclust: Normal Mixture Modeling for Model...
  • MiniSat

  • Referenced in 558 articles [sw00577]
  • An extensible SAT-solver. MiniSat is a minimalistic...
  • R

  • Referenced in 9188 articles [sw00771]
  • R is a language and environment for statistical...
  • STAR

  • Referenced in 14 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • NEURON

  • Referenced in 186 articles [sw03059]
  • Parallel network simulations with NEURON. The NEURON simulation...
  • CUDA

  • Referenced in 1288 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...