• DNAshapeR

  • Referenced in 0 articles [sw18973]
  • shape prediction and feature encoding. Summary: DNAshapeR predicts DNA shape features in an ultra-fast ... visualization and further analysis. DNAshapeR further encodes DNA sequence and shape features as user-defined...
  • MEME

  • Referenced in 14 articles [sw15711]
  • ungapped sequence patterns that occur in the DNA or protein sequences provided by the user ... search sequence databases for matches to motifs encoded in several popular formats. By clicking...
  • gclust

  • Referenced in 0 articles [sw17410]
  • DNA sequences from the mitochondrially encoded NADH dehydrogenase 3 (ND3) gene of a collection...
  • dna2vec

  • Referenced in 1 article [sw18696]
  • DNA sequence is dividing it into shorter k-mer components. Unfortunately, the straightforward vector encoding...
  • BiRen

  • Referenced in 1 article [sw27676]
  • Motivation: Enhancer elements are noncoding stretches of DNA that play key roles in controlling gene ... enhancers and deciphering the transcriptional regulatory code encoded in the enhancer sequences is urgent. Results ... architecture, BiRen, which predicts enhancers using the DNA sequence alone. Our results demonstrate that BiRen...
  • ProSOM

  • Referenced in 3 articles [sw13019]
  • promoter prediction based on unsupervised clustering of DNA physical profiles. Motivation: More and more genomes ... round performance. Additional tests on the ENCODE regions of the human genome show that...
  • GLUE-IT

  • Referenced in 3 articles [sw33402]
  • library diversity at the protein (rather than DNA) level. We have now updated ... Calculator, for finding degenerate codons that encode user-specified sets of amino acids. We also...
  • PEDEL-AA

  • Referenced in 3 articles [sw33403]
  • library diversity at the protein (rather than DNA) level. We have now updated ... Calculator, for finding degenerate codons that encode user-specified sets of amino acids. We also...
  • DGW

  • Referenced in 1 article [sw33138]
  • like ChIP-seq for the detection of DNA-protein interactions. These techniques return large, high ... real epigenomic data set from the ENCODE project. Conclusions: Our results show that DGW automatically...
  • ModeRNA

  • Referenced in 1 article [sw17142]
  • structure and dynamics, which in turn is encoded in the linear sequence. However, while there ... modifications in proteins. ModeRNA can also model DNA structures or use them as templates...
  • Magma

  • Referenced in 2720 articles [sw00540]
  • Computer algebra system (CAS). Magma is a large...
  • Maple

  • Referenced in 4933 articles [sw00545]
  • The result of over 30 years of cutting...
  • Matlab

  • Referenced in 11547 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 7694 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1511 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • STAR

  • Referenced in 11 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • CUDA

  • Referenced in 1138 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...
  • SPIN

  • Referenced in 699 articles [sw03455]
  • Spin is a popular open-source software tool...
  • SDPT3

  • Referenced in 597 articles [sw04009]
  • This software is designed to solve conic programming...