• KEGG

  • Referenced in 180 articles [sw13866]
  • Kyoto Encyclopedia of Genes and Genomes. KEGG is a database resource for understanding high-level ... cell, the organism and the ecosystem, from genomic and molecular-level information...
  • UniProt

  • Referenced in 88 articles [sw21320]
  • exists in the database with the majority of sequences coming from genome sequencing projects...
  • JASPAR

  • Referenced in 24 articles [sw18502]
  • database for eukaryotic transcription factor binding profiles. The analysis of regulatory regions in genome sequences ... scoring matrices. JASPAR is an open‐access database of annotated, high‐quality, matrix‐based transcription ... experimentally demonstrated to bind transcription factors. The database is complemented by a web interface ... suite of programming tools for genome‐wide and comparative genomic analysis of regulatory regions. JASPAR...
  • Galaxy

  • Referenced in 8 articles [sw16927]
  • that combines the power of existing genome annotation databases with a simple Web portal...
  • SMART

  • Referenced in 14 articles [sw17187]
  • predicted proteins from complete genomes in its source sequence databases, and integrates these with predictions...
  • TRANSFAC

  • Referenced in 16 articles [sw17201]
  • regulation. TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding ... proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs...
  • MAKER

  • Referenced in 2 articles [sw17331]
  • independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins ... GMOD database. Its outputs can also be viewed in the Apollo Genome browser; this feature ... mediterranea and to create a new genome database, SmedGD. We have also compared MAKER ... genome sequence into a community-accessible genome database. MAKER should prove especially useful for emerging...
  • GOLD

  • Referenced in 4 articles [sw23027]
  • Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs ... range of Sequencing Projects (such as isolate genome, single-cell genome, metagenome, metatranscriptome) and complex...
  • QGRS mapper

  • Referenced in 2 articles [sw27630]
  • from fully annotated entries of public genomic databases (GenBank/RefSeq), search transcribed regions of the genes...
  • FORESST

  • Referenced in 2 articles [sw26866]
  • program will allow rapid screening of genomic databases and sequence annotation when fold similarity...
  • TFGD

  • Referenced in 1 article [sw18850]
  • Tomato functional genomics database: a comprehensive resource and analysis package for tomato functional genomics. Tomato ... Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize ... integrate large-scale tomato functional genomics data sets. The database is functionally expanded from ... sRNA data sets archived in the database, respectively, and TFGD provides downloads...
  • GtRNAdb

  • Referenced in 2 articles [sw23001]
  • expanded database of transfer RNA genes identified in complete and draft genomes. Transfer RNAs represent ... tRNA genes in genomes, and the Genomic tRNA Database (GtRNAdb) was created as a portal ... number of tRNA predictions (>367000) and genomes analyzed (>4370), but more importantly, the integration ... direct links to the UCSC genome browsers. The database can be searched by sequence...
  • TabSQL

  • Referenced in 1 article [sw18563]
  • data to public databases. Background: With advances in high-throughput genomics and proteomics ... their data to annotations in public databases. Results: We developed TabSQL, a MySQL-based application ... database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site...
  • GenBank

  • Referenced in 4 articles [sw28961]
  • GenBank® (http://www.ncbi.nlm.nih.gov) is a comprehensive database that contains publicly available nucleotide sequences for almost ... from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most ... major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain ... similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates...
  • GARSA

  • Referenced in 1 article [sw17184]
  • information from several bioinformatics tools and genomic databases, in a flexible way. GARSA ... friendly web-based system designed to analyze genomic data in the context of a pipeline...
  • yOWL

  • Referenced in 1 article [sw24081]
  • yeast data obtained from the Saccharomyces Genome Database and UniProt, we discuss the challenges encountered...
  • fastWKendall

  • Referenced in 1 article [sw27812]
  • huge-volume datasets, such as genome databases, streaming stock market data, and publicly available huge...
  • MAExplorer

  • Referenced in 1 article [sw08354]
  • analysis methods and access to new genomic databases as they become available. MAExplorer was implemented...
  • PAComplex

  • Referenced in 1 article [sw21769]
  • these hit templates from complete pathogen genome databases (≥10(8) peptide candidates from...
  • Bambino

  • Referenced in 2 articles [sw17426]
  • genome annotation features from a UCSC genome annotation database, display histograms of non-reference allele...