• BLAST

  • Referenced in 241 articles [sw17334]
  • similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases...
  • fastDNAml

  • Referenced in 92 articles [sw06651]
  • estimating maximum likelihood phylogenetic trees from nucleotide sequences. Much of this program is based...
  • ape

  • Referenced in 55 articles [sw04569]
  • macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several...
  • TRANSFAC

  • Referenced in 73 articles [sw17201]
  • training sequences used for the construction of nucleotide matrices as well as by data...
  • Cd-hit

  • Referenced in 46 articles [sw16887]
  • comparing large sets of protein or nucleotide sequences. Motivation: In 2001 and 2002, we published ... compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences...
  • iRNA-PseColl

  • Referenced in 30 articles [sw24441]
  • Modifications by Incorporating Collective Effects of Nucleotides into PseKNC. There are many different types ... elements into the general pseudo K-tuple nucleotide composition (PseKNC) of RNA via the chemicophysical ... properties and density distribution of its constituent nucleotides. Rigorous cross-validations have indicated that...
  • iPro54-PseKNC

  • Referenced in 32 articles [sw22411]
  • promoters in prokaryote with pseudo k-tuple nucleotide composition. The σ(54) promoters are unique ... novel feature vector called ’pseudo k-tuple nucleotide composition’, which was further optimized...
  • iNuc-PseKNC

  • Referenced in 31 articles [sw16607]
  • positioning in genomes with pseudo k-tuple nucleotide composition. Motivation: Nucleosome positioning participates in many ... novel feature-vector called ‘pseudo k-tuple nucleotide composition’, into which six DNA local structural...
  • PseKNC

  • Referenced in 31 articles [sw22436]
  • server for generating pseudo K-tuple nucleotide composition. The pseudo oligonucleotide composition, or pseudo ... tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with...
  • MAFFT

  • Referenced in 41 articles [sw08304]
  • Multiple alignment program for amino acid or nucleotide sequences. MAFFT is a multiple sequence alignment...
  • JASPAR

  • Referenced in 40 articles [sw18502]
  • profiles were derived exclusively from sets of nucleotide sequences experimentally demonstrated to bind transcription factors...
  • iRNA-AI

  • Referenced in 26 articles [sw24437]
  • incorporating the chemical properties of nucleotides and their sliding occurrence density distribution along ... sequence into the general form of pseudo nucleotide composition (PseKNC). It has been shown...
  • 2L-piRNA

  • Referenced in 25 articles [sw27667]
  • Here, by incorporating the physicochemical properties of nucleotides into the pseudo K-tuple nucleotide composition...
  • iDNA6mA-PseKNC

  • Referenced in 21 articles [sw27663]
  • Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC. N6-methyladenine ... iDNA6mA-PseKNC that is established by incorporating nucleotide physicochemical properties into Pseudo K-tuple Nucleotide...
  • Seq-Gen

  • Referenced in 30 articles [sw08310]
  • program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny...
  • iEnhancer-2L

  • Referenced in 21 articles [sw18831]
  • their strength by pseudo k -tuple nucleotide composition. Motivation: Enhancers are of short regulatory ... elements with the ‘pseudo k -tuple nucleotide composition’, into which the six DNA local parameters...
  • iRSpot-EL

  • Referenced in 29 articles [sw24776]
  • fusing different modes of pseudo K-tuple nucleotide composition and mode of dinucleotide-based auto...
  • iRNA-PseU

  • Referenced in 19 articles [sw27659]
  • proposed by incorporating the chemical properties of nucleotides and their occurrence frequency density distributions into ... general form of pseudo nucleotide composition (PseKNC). It has been demonstrated via the rigorous jackknife...
  • iPromoter-2L

  • Referenced in 22 articles [sw24788]
  • multi-window-based PseKNC (pseudo K-tuple nucleotide composition) approach to incorporate the short-, middle...
  • Kalign

  • Referenced in 13 articles [sw13194]
  • high-performance multiple alignment of protein and nucleotide sequences allowing external features. In the growing ... alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows ... protein alignments while its accuracy on nucleotide alignments is generally superior. In addition, we demonstrate...