• PSI-BLAST

  • Referenced in 226 articles [sw17324]
  • tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety...
  • iRSpot-PseDNC

  • Referenced in 65 articles [sw22437]
  • time-consuming. With the avalanche of genome sequences generated in the postgenomic ... 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...
  • MUMMER

  • Referenced in 39 articles [sw17256]
  • fast alignment of large-scale DNA and protein sequences. MUMmer is a system for rapidly ... 1000s of contigs from a shotgun sequencing project, and will align them to another ... species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer...
  • iNuc-PseKNC

  • Referenced in 31 articles [sw16607]
  • cellular processes. With the avalanche of genome sequences generated in the post-genomic ... 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...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • modes of pseudo components of DNA, RNA, and protein sequences. With the avalanche of biological ... effectively formulate the sequence of a biological sample (such as DNA, RNA or protein) with ... vector that can effectively reflect its sequence pattern information or capture its key features concerned ... possible feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those...
  • iRSpot-TNCPseAAC

  • Referenced in 31 articles [sw22412]
  • opposite aspects that coexist in a DNA system. As a driving force for evolution ... With the ever-increasing amount of genome sequence data in the postgenomic era, computational methods ... predictor called “iRSpot-TNCPseAAC”, in which a DNA sample was formulated by combining its trinucleotide ... aforementioned novel approach to incorporate the DNA sequence order information into a discrete model...
  • iPro54-PseKNC

  • Referenced in 32 articles [sw22411]
  • related genes. With the avalanche of genome sequences generated in the postgenomic ... predictor, the samples of DNA sequences were formulated by a novel feature vector called ’pseudo...
  • iPromoter-2L

  • Referenced in 22 articles [sw24788]
  • urgent in facing the avalanche of DNA sequences discovered in the postgenomic age. Although some ... incorporate the short-, middle-, and long-range sequence information, we have developed a two-layer ... layer serves to identify a query DNA sequence as a promoter or non-promoter...
  • DNASequenceGenerator

  • Referenced in 17 articles [sw01285]
  • program for the construction of DNA sequences In DNA Computing and DNA nanotechnology the design ... proper DNA sequences turned out to be an elementary problem. We here present a software ... construction of sets (“pools”) of DNA sequences. The program can create DNA sequences to meet...
  • iEnhancer-2L

  • Referenced in 21 articles [sw18831]
  • 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...
  • 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...
  • iDNA-Methyl

  • Referenced in 19 articles [sw22423]
  • drug development. Given an uncharacterized DNA sequence containing many cytosine residues, which ... cannot? With the avalanche of DNA sequences generated during the postgenomic age, it is highly ... accurately identifying the methylation sites in DNA. Using the trinucleotide composition, pseudo amino acid components...
  • GATK

  • Referenced in 14 articles [sw12019]
  • MapReduce framework for analyzing next-generation DNA sequencing data. Next-generation DNA sequencing (NGS) projects ... robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce...
  • repDNA

  • Referenced in 12 articles [sw16473]
  • various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties ... suitable approach to effectively represent the DNA sequences. To facilitate the studies of DNAs ... correlation between two oligonucleotides along a DNA sequence in terms of their specific physicochemical properties ... used to represent a DNA sequence with a discrete model or vector yet still keep...
  • iDNA6mA-PseKNC

  • Referenced in 21 articles [sw27663]
  • occurring in a wide range of DNA sequences. Accurate identification of its sites will...
  • PseKNC

  • Referenced in 31 articles [sw22436]
  • used to represent a DNA or RNA sequence with a discrete model or vector ... computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems ... useful tool in computational genomics and genome sequence analysis...
  • PAML

  • Referenced in 40 articles [sw10916]
  • programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained...
  • MEGA

  • Referenced in 32 articles [sw09078]
  • software for evolutionary analysis of DNA and protein sequences. The Molecular Evolutionary Genetics Analysis (MEGA ... designed for comparative analysis of homologous gene sequences either from multigene families or from different ... inferring evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools ... many convenient facilities for the assembly of sequence data sets from files or web-based...
  • MEGAN

  • Referenced in 17 articles [sw33189]
  • clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving ... preprocessing step, the set of DNA sequences is compared against databases of known sequences using...
  • InterProScan

  • Referenced in 17 articles [sw17336]
  • application. Protein as well as DNA sequences can be analysed. A web-based version...