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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.