• KEGG

  • Referenced in 262 articles [sw13866]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG is a database resource for understanding high ... cell, the organism and the ecosystem, from genomic and molecular-level information ... molecular building blocks of genes and proteins (genomic information) and chemical substances (chemical information) that...
  • Bioconductor

  • Referenced in 307 articles [sw04205]
  • analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language...
  • UniProt

  • Referenced in 131 articles [sw21320]
  • with the majority of sequences coming from genome sequencing projects. We have created...
  • iRSpot-PseDNC

  • Referenced in 65 articles [sw22437]
  • variations. Rather than randomly occurring across a genome, meiotic recombination takes place in some genomic ... mechanism of recombination and the genome evolution process as well. So far, the recombination regions ... time-consuming. With the avalanche of genome sequences generated in the postgenomic ... extended to deal with all the other genomes. Particularly, it has not escaped our notice...
  • PMA

  • Referenced in 114 articles [sw19126]
  • sparse canonical correlation analysis, with applications to genomic data. Statistical Applications in Genetics and Molecular...
  • PHYLIP

  • Referenced in 100 articles [sw07694]
  • Felsenstein of the Department of Genome Sciences and the Department of Biology at the University...
  • TRANSFAC

  • Referenced in 74 articles [sw17201]
  • database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/...
  • MUMMER

  • Referenced in 40 articles [sw17256]
  • system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer ... matches between a pair of 5-megabase genomes in 13.7 seconds, using ... desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s ... another set of contigs or a genome using the NUCmer program included with the system...
  • BLAT

  • Referenced in 36 articles [sw16891]
  • BLAST-Like Alignment Tool. Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments ... nonoverlapping K-mers in the genome. This index fits inside the RAM of inexpensive computers ... need only be computed once for each genome assembly. BLAT has several major stages ... index to find regions in the genome likely to be homologous to the query sequence...
  • JASPAR

  • Referenced in 42 articles [sw18502]
  • profiles. The analysis of regulatory regions in genome sequences is strongly based on the detection ... suite of programming tools for genome‐wide and comparative genomic analysis of regulatory regions. JASPAR...
  • BWA

  • Referenced in 47 articles [sw34374]
  • divergent sequences against a large reference genome, such as the human genome. It consists...
  • ArrayExpress

  • Referenced in 40 articles [sw29723]
  • ArrayExpress - functional genomics data. ArrayExpress Archive of Functional Genomics Data stores data from high-throughput ... functional genomics experiments, and provides these data for reuse to the research community...
  • PLINK

  • Referenced in 63 articles [sw04581]
  • PLINK is a free, open-source whole genome association analysis toolset, designed to perform...
  • iNuc-PseKNC

  • Referenced in 31 articles [sw16607]
  • based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. Motivation ... regulating cellular processes. With the avalanche of genome sequences generated in the post-genomic ... Homo sapiens, Caenorhabditis elegans and Drosophila melanogaster genomes, respectively. In the new predictor, the samples ... nucleosome positioning of the aforementioned three genomes were 86.27%, 86.90% and 79.97%, respectively. Meanwhile...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • biological sequences generated in the post-genomic age, one of the most challenging problems ... very useful tool in computational proteomics, genomics, as well as biological sequence analysis. Moreover...
  • iRSpot-TNCPseAAC

  • Referenced in 31 articles [sw22412]
  • recombination does not occur randomly across a genome, but with higher probability in some genomic ... coldspots”. With the ever-increasing amount of genome sequence data in the postgenomic era, computational ... meiotic recombination and the process of genome evolution as well. To meet the need ... also be used for many other genome analysis problems. The web-server for iRSpot-TNCPseAAC...
  • PseKNC

  • Referenced in 31 articles [sw22436]
  • dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different ... become a very useful tool in computational genomics and genome sequence analysis...
  • ARACNE

  • Referenced in 36 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...
  • 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...
  • edgeR

  • Referenced in 49 articles [sw06936]
  • near future for many functional genomics applications. One of the fundamental data analysis tasks, especially...