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Table 1 Genomics Resources

From: Touring Ensembl: A practical guide to genome browsing

Name Website Function
Genome Browsing
Ensembl
http://www.ensembl.org Genome browser and annotation (chordates)
Ensembl Genomes http://www.ensemblgenomes.org Genome browser and annotation (nonchordates)
Gbrowse http://flybase.net/cgi-bin/gbrowse/dmel/ Genome browser and annotation (fruit fly)
NCBI Map Viewer http://www.ncbi.nlm.nih.gov/mapview/ Genome browser and annotation (multi-species)
NCBI Sequence Viewer http://www.ncbi.nlm.nih.gov Genome browser and annotation (multi-species)
UCSC Browser http://genome.ucsc.edu/ Genome browser and annotation (multi-species)
VISTA Enhancer Browser http://enhancer.lbl.gov/ Non-coding elements (human)
1000 Genomes Browser http://browser.1000genomes.org/ Genome browser (human, multiple individuals)
IGB http://tinyurl.com/n83lnn Visualization tool (multiple sources)
IGV http://www.broadinstitute.org/igv/ Visualization tool (multiple sources)
DAS
DAS Registry
http://www.dasregistry.org/ DAS sources available
Ensembl DAS list http://www.ensembl.org/das/dsn DAS sources available in Ensembl
Protein and Nucleotides RefSeq http://www.ncbi.nlm.nih.gov/RefSeq Repository of nucleic acid and protein sequences
UniProt http://www.uniprot.org Repository of protein sequence (manually curated)
Tools
BioMart
http://www.biomart.org Data mining tool for export of tables and sequences
EMBOSS http://emboss.sourceforge.net/ Open source software for molecular biology
TreeBest http://treesoft.sourceforge.net/njtree.shtml Construction and analysis of phylogenetic trees
Regulatory Features CisRed http://www.cisred.org Database: Regulatory sequences
DNase I Footprint http://www.flyreg.org Database: Transcription factor binding sites (fly)
miRanda http://www.microrna.org Database: miRNA targets (multi-species)
  1. Major genomics resources with links to websites.