• BioProspector

  • Referenced in 28 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...
  • ARACNE

  • Referenced in 32 articles [sw17200]
  • pathologic phenotypes. Existing computational methods for the genome-wide ”reverse engineering” of such networks have ... successful only for lower eukaryotes with simple genomes. Here we present ARACNE, a novel algorithm...
  • 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...
  • clustervalidation

  • Referenced in 28 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...
  • 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...
  • TopHat

  • Referenced in 22 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...
  • E-CELL

  • Referenced in 20 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...
  • 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...
  • 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...
  • pi-MASS

  • Referenced in 16 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...
  • iEnhancer-2L

  • Referenced in 21 articles [sw18831]
  • sequences generated in the post-genomic age, it is a challenging task to develop computational ... potential to become a useful tool for genome analysis. Availability and implementation: For the convenience...
  • SSS

  • Referenced in 29 articles [sw07794]
  • discuss an example from gene expression cancer genomics, comparisons with MCMC and other methods...
  • OrthoMCL

  • Referenced in 14 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...
  • GCTA

  • Referenced in 16 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...
  • MetaCyc

  • Referenced in 28 articles [sw08243]
  • metabolic pathways of organisms from their sequenced genomes, supporting metabolic engineering, helping to compare biochemical...
  • SHRiMP

  • Referenced in 15 articles [sw17146]
  • opening the door to population genomic studies of non-model species. In this paper ... methods to map short reads to a genome, even in the presence of a large ... sequenced Ciona savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately ... reads to this highly polymorphic genome, while confirming high heterozygosity of C. savignyi in this...
  • SMART

  • Referenced in 16 articles [sw17187]
  • SMART 4.0: towards genomic data integration. SMART (Simple Modular Architecture Research Tool ... integration of data from completed metazoan genomes. SMART now uses predicted proteins from complete genomes...
  • iRNA-3typeA

  • Referenced in 16 articles [sw27660]
  • functions and mechanisms and for treating some genomic diseases as well. With the avalanche ... sequences generated in the post-genomic age, many computational methods have been proposed for identifying ... become a useful high throughput tool for genome analysis...
  • GATK

  • Referenced in 13 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...