• PatternHunter

  • Referenced in 36 articles [sw20963]
  • faster and more sensitive homology search. MOTIVATION: Genomics and proteomics studies routinely depend on homology ... matches which are then extended. The exploding genomic data growth presents a dilemma...
  • clustervalidation

  • Referenced in 35 articles [sw34195]
  • Computational cluster validation in post-genomic data analysis. Results: This review paper aims to familiarize ... particular focus on their application to post-genomic data analysis. Synthetic and real biological datasets...
  • BioProspector

  • Referenced in 29 articles [sw09375]
  • expressed genes. The development of high throughput genome sequencing and gene expression techniques gives rise ... sequences or pre-computed from the whole genome sequences. A new motif scoring function ... find s54 motif from M. xanthus genome, many B. subtilis motifs from DBTBS collection...
  • iPro54-PseKNC

  • Referenced in 32 articles [sw22411]
  • promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes ... With the avalanche of genome sequences generated in the postgenomic age, it is highly desired...
  • ranger

  • Referenced in 42 articles [sw14498]
  • analyze data on the scale of a genome-wide association study...
  • Memtype-2L

  • Referenced in 39 articles [sw16472]
  • protein sequences generated in the Post-Genomic Age and the relatively much slower progress...
  • iSNO-PseAAC

  • Referenced in 39 articles [sw22446]
  • protein sequences generated in the post-genomic age, it is highly desired to develop computational...
  • GCTA

  • Referenced in 22 articles [sw23135]
  • GCTA: a tool for genome-wide complex trait analysis. For most human complex diseases ... traits, SNPs identified by genome-wide association studies (GWAS) explain only a small fraction ... report a user-friendly software tool called genome-wide complex trait analysis (GCTA), which ... chromosome or on the whole genome for a complex trait rather than testing the association...
  • SSS

  • Referenced in 38 articles [sw07794]
  • discuss an example from gene expression cancer genomics, comparisons with MCMC and other methods...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • software environment for whole-cell simulation. MOTIVATION: Genome sequencing projects and further systematic functional analyses ... smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR ... CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available...
  • TopHat

  • Referenced in 23 articles [sw17157]
  • length indels with respect to the reference genome. In addition to de novo spliced alignment ... across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify ... accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2...
  • pi-MASS

  • Referenced in 20 articles [sw17249]
  • Bayesian variable selection regression for genome-wide association studies and other large-scale problems ... Bayesian Variable Selection Regression, or BVSR, to genome-wide association studies and similar large-scale ... regression problems. Currently, typical genome-wide association studies measure hundreds of thousands, or millions ... covariates in the regression. Characteristic features of genome-wide association studies include the following...
  • Mauve

  • Referenced in 16 articles [sw24606]
  • Mauve: multiple alignment of conserved genomic sequence with rearrangements. As genomes evolve, they undergo large ... posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into ... chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic ... regions shared with a subset of other genomes and segments conserved among all the genomes...
  • 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 ... data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make ... these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed...
  • Bowtie 2

  • Referenced in 20 articles [sw29190]
  • aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with ... memory footprint small: for the human genome, its memory footprint is typically around...
  • Velvet

  • Referenced in 31 articles [sw17026]
  • Velvet,” to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph...
  • JIVE

  • Referenced in 22 articles [sw09511]
  • objects. In particular, The Cancer Genome Atlas (TCGA) includes data from several diverse genomic technologies...
  • iPromoter-2L

  • Referenced in 22 articles [sw24788]
  • initiating transaction of a particular gene in genome, promoter is a short region ... very useful high throughput tool for genome analysis...
  • OrthoMCL

  • Referenced in 15 articles [sw29602]
  • OrthoMCL: identification of ortholog groups for eukaryotic genomes. The identification of orthologous groups is useful ... genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences ... Methods successfully exploited for prokaryotic genome analysis have proved difficult to apply to eukaryotes, however ... larger genomes may contain multiple paralogous genes, and sequence information is often incomplete. OrthoMCL provides...
  • REPuter

  • Referenced in 17 articles [sw29724]
  • manifold applications of repeat analysis on a genomic scale. The repetitive structure of genomic ... systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic...