• JASPAR

  • Referenced in 42 articles [sw18502]
  • factor binding profiles. The analysis of regulatory regions in genome sequences is strongly based ... searching and subset selection, an online sequence analysis utility and a suite of programming tools...
  • PseKNC

  • Referenced in 31 articles [sw22436]
  • problems in computational genomics and genome sequence analysis. However, dealing with different ... tool in computational genomics and genome sequence analysis...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those feature ... learning algorithms to develop computational predictors and analysis methods for various tasks in bioinformatics ... proteomics, genomics, as well as biological sequence analysis. Moreover, to maximize users’ convenience, its stand...
  • EMBOSS

  • Referenced in 35 articles [sw10917]
  • EMBOSS is a free Open Source software analysis package specially developed for the needs ... formats and even allows transparent retrieval of sequence data from the web. Also, as extensive ... currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks...
  • MEGA

  • Referenced in 35 articles [sw09078]
  • centric software for evolutionary analysis of DNA and protein sequences. The Molecular Evolutionary Genetics Analysis ... desktop application designed for comparative analysis of homologous gene sequences either from multigene families ... statistical analysis of data, MEGA provides many convenient facilities for the assembly of sequence data...
  • BEAST

  • Referenced in 59 articles [sw12588]
  • platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies...
  • REPuter

  • Referenced in 17 articles [sw29724]
  • applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy...
  • rjags

  • Referenced in 65 articles [sw08039]
  • data analysis. JAGS uses Markov Chain Monte Carlo (MCMC) to generate a sequence of dependent...
  • MEGAN

  • Referenced in 17 articles [sw33189]
  • MEGAN analysis of metagenomic data. Metagenomics is the study of the genomic content ... common habitat using targeted or random sequencing. Goals include understanding the extent and role ... sequence databases of known sequences. Most published studies use the analysis of paired-end reads ... analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences...
  • MAVG

  • Referenced in 9 articles [sw10918]
  • applications in several areas of biomolecular sequence analysis including locating GC-rich regions...
  • GloptiPoly

  • Referenced in 327 articles [sw04343]
  • mathematics such as algebra, Fourier analysis, functional analysis, operator theory, probability and statistics, to cite ... relaxations of the GPM, whose associated monotone sequence of optimal values converges to the global...
  • qLearn

  • Referenced in 20 articles [sw11117]
  • Archive Network (http://cran.r-project.org/). Analysis of the Sequenced Treatment Alternatives to Relieve Depression (STAR...
  • bioNMF

  • Referenced in 6 articles [sw14438]
  • been successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining ... that implements the NMF methodology in different analysis contexts to support some of the most ... biclustering gene expression data, protein sequence analysis, text mining of biomedical literature and sample classification...
  • 2D-MH

  • Referenced in 21 articles [sw19727]
  • acids. Introduction of graphic representation for biological sequences can provide intuitive overall pictures as well ... useful insights for performing large-scale analysis. Here, a new two-dimensional graph, called ... proposed to represent protein sequences. It is formed by incorporating the information of the side ... vehicle for large-scale analysis of the avalanche of protein sequences generated in the post...
  • ExPASy

  • Referenced in 14 articles [sw34228]
  • prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools...
  • RAST

  • Referenced in 8 articles [sw17158]
  • resource for the automatic phylogenetic and functional analysis of metagenomes. Background: Random community genomes (metagenomes ... with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing ... pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein ... primary bottlenecks in metagenome sequence analysis – the availability of high-performance computing for annotating...
  • UniProt

  • Referenced in 136 articles [sw21320]
  • help users track the provenance of sequences. We present a new website that has been ... best characterized and most informative for comparative analysis. All UniProt data is provided freely...
  • GATK

  • Referenced in 17 articles [sw12019]
  • genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Next-generation ... sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding ... make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals ... efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy...
  • CkAnalytic

  • Referenced in 11 articles [sw19313]
  • Computer assisted Fourier analysis in sequence spaces of varying regularity. This work treats a functional ... analytic framework for computer assisted Fourier analysis which can be used to obtain mathematically rigorous ... main tools are certain infinite sequence spaces of rapidly decaying coefficients: we employ sequence spaces...
  • SeqAn

  • Referenced in 6 articles [sw19473]
  • efficient, generic C++ library for sequence analysis. SeqAn is an open source C++ library ... algorithms and data structures for the analysis of sequences with the focus on biological data...