• REPuter

  • Referenced in 17 articles [sw29724]
  • applications of repeat analysis on a genomic scale. The repetitive structure of genomic DNA holds ... genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein...
  • FatiGO

  • Referenced in 21 articles [sw12318]
  • genes within the context of a genome-scale experiment (DNA microarray, proteomics, etc.). Said procedure...
  • BiGG

  • Referenced in 10 articles [sw17247]
  • large scale metabolic reconstructions. Background: Genome-scale metabolic reconstructions under the Constraint Based Reconstruction ... Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome...
  • Notung

  • Referenced in 13 articles [sw08917]
  • Duplications and Optimizing Gene Family Tree. Large scale gene duplication is a major force driving ... evolution of genetic functional innovation. Whole genome duplications are widely believed to have played ... soon allow similar studies on a genomic scale, but such studies will be limited unless...
  • COBRA Toolbox

  • Referenced in 13 articles [sw32083]
  • variety of metabolic phenotypes using genome-scale biochemical networks...
  • ranger

  • Referenced in 33 articles [sw14498]
  • analyze data on the scale of a genome-wide association study...
  • Galaxy

  • Referenced in 12 articles [sw16927]
  • Galaxy: A platform for interactive large-scale genome analysis. Accessing and analyzing the exponentially expanding...
  • TM4

  • Referenced in 12 articles [sw26846]
  • studying gene expression on a genomic scale. Advances in the precision of array printers...
  • GAGE

  • Referenced in 11 articles [sw13528]
  • evaluation of the very latest large-scale genome assembly algorithms. We have organized this ”bake...
  • pi-MASS

  • Referenced in 16 articles [sw17249]
  • selection regression for genome-wide association studies and other large-scale problems We consider applying ... studies and similar large-scale regression problems. Currently, typical genome-wide association studies measure hundreds ... issue of “missing heritability” in genome-wide association studies. More generally, we demonstrate that, despite ... provide useful inferences in these large-scale problems, and in our simulations produces better power...
  • BaCelLo

  • Referenced in 9 articles [sw17174]
  • subcellular location of proteins in large scale genomic projects. Results. BaCelLo is a predictor...
  • PLINK

  • Referenced in 64 articles [sw04581]
  • whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses...
  • MSOAR

  • Referenced in 7 articles [sw29658]
  • between closely related species on a genome scale. It attempts to reconstruct the evolutionary history...
  • CMfinder

  • Referenced in 6 articles [sw17265]
  • coding RNAs and computational advances in genome-scale RNA search create a need for tools...
  • MUMMER

  • Referenced in 40 articles [sw17256]
  • scale DNA and protein sequences. MUMmer is a system for rapidly aligning entire genomes, whether...
  • MetExplore

  • Referenced in 4 articles [sw12274]
  • allows to build, curate and analyse genome-scale metabolic networks. MetExplore stores metabolic networks ... identify compounds from masses. Several genome-scale models designed for Flux Balance Analysis have also...
  • F2c2

  • Referenced in 3 articles [sw17352]
  • computation of flux coupling in gen ome-scale metabolic networks. Background: Flux coupling analysis ... constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes ... approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed ... computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available...
  • FindPeaks

  • Referenced in 7 articles [sw29575]
  • protein–DNA association events on a genome-wide scale, and is being applied...
  • OligoArray

  • Referenced in 3 articles [sw36133]
  • that designs specific oligonucleotides at the genomic scale. It uses a thermodynamic approach to predict ... perform expression analysis on a genomic scale for any organism for which the genome sequence...
  • COBRApy

  • Referenced in 3 articles [sw16711]
  • COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes ... leading software package for genome-scale analysis of metabolism; however, it was not designed...