• PSI-BLAST

  • Referenced in 231 articles [sw17324]
  • widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons...
  • Cytoscape

  • Referenced in 76 articles [sw09080]
  • with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available ... protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction...
  • iRSpot-PseDNC

  • Referenced in 65 articles [sw22437]
  • predictor, the samples of DNA sequences are formulated by a novel feature vector ... dinucleotide composition’ (PseDNC), into which six local DNA structural properties, i.e. three angular parameters (twist ... also used to study many other DNA-related problems. As a user-friendly web-server...
  • impute

  • Referenced in 99 articles [sw14376]
  • Missing value estimation for DNA microarrays. Motivation: Gene expression microarray experiments can generate data sets...
  • TRANSFAC

  • Referenced in 74 articles [sw17201]
  • transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/ ). Its content...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • generating various modes of pseudo components of DNA, RNA, and protein sequences. With the avalanche ... sequence of a biological sample (such as DNA, RNA or protein) with a discrete model ... nearly all the possible feature vectors for DNA, RNA and protein sequences. Particularly...
  • MUMMER

  • Referenced in 40 articles [sw17256]
  • MUMmer Ultra-fast alignment of large-scale DNA and protein sequences. MUMmer is a system ... species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer...
  • iRSpot-TNCPseAAC

  • Referenced in 31 articles [sw22412]
  • opposite aspects that coexist in a DNA system. As a driving force for evolution ... predictor called “iRSpot-TNCPseAAC”, in which a DNA sample was formulated by combining its trinucleotide ... PseAAC) of the protein translated from the DNA sample according to its genetic codes ... aforementioned novel approach to incorporate the DNA sequence order information into a discrete model...
  • iNuc-PseKNC

  • Referenced in 31 articles [sw16607]
  • determining the nucleosome positioning on a DNA sequence. Results: Here a predictor called ‘iNuc-PseKNC ... predictor, the samples of DNA sequences were formulated by a novel feature-vector called ‘pseudo ... tuple nucleotide composition’, into which six DNA local structural properties were incorporated. It was observed...
  • MEGA

  • Referenced in 34 articles [sw09078]
  • biologist-centric software for evolutionary analysis of DNA and protein sequences. The Molecular Evolutionary Genetics ... inferring evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools...
  • DIALIGN

  • Referenced in 33 articles [sw12015]
  • DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. DIALIGN is a widely used software ... tool for multiple DNA and protein sequence alignment. The program combines local and global alignment...
  • PseKNC

  • Referenced in 31 articles [sw22436]
  • PseKNC), can be used to represent a DNA or RNA sequence with a discrete model ... genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds...
  • PAML

  • Referenced in 42 articles [sw10916]
  • package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood...
  • iEnhancer-2L

  • Referenced in 22 articles [sw18831]
  • composition. Motivation: Enhancers are of short regulatory DNA elements. They can be bound with proteins ... transcription in eukaryotes. With the avalanche of DNA sequences generated in the post-genomic ... timely identifying enhancers from extremely complicated DNA sequences. Although some efforts have been made ... limited at only identifying whether a query DNA element being of an enhancer...
  • Mfold

  • Referenced in 41 articles [sw12672]
  • provide easy access to RNA and DNA folding and hybridization software to the scientific community...
  • iRSpot-EL

  • Referenced in 28 articles [sw24776]
  • ensemble learning approach. MOTIVATION: Coexisting in a DNA system, meiosis and recombination are two indispensible ... urgent challenge to acquire the information of DNA recombination spots because it can timely provide...
  • iDNA-Methyl

  • Referenced in 19 articles [sw22423]
  • iDNA-Methyl: identifying DNA methylation sites via pseudo trinucleotide composition. Predominantly occurring on cytosine ... DNA methylation is a process by which cells can modify their DNAs to change ... types of cancer. Therefore, knowledge of DNA methylation sites is significant for both basic research ... drug development. Given an uncharacterized DNA sequence containing many cytosine residues, which...
  • iPromoter-2L

  • Referenced in 23 articles [sw24788]
  • genome, promoter is a short region of DNA. Promoters have various types with different functions ... urgent in facing the avalanche of DNA sequences discovered in the postgenomic age. Although some ... first layer serves to identify a query DNA sequence as a promoter or non-promoter...
  • PatternHunter

  • Referenced in 36 articles [sw20963]
  • genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases...
  • iPro54-PseKNC

  • Referenced in 34 articles [sw22411]
  • developed. In the predictor, the samples of DNA sequences were formulated by a novel feature...