Table 1

Genomics Resources

Name

Website

Function


    Genome Browsing

Ensembl

http://www.ensembl.org webcite

Genome browser and annotation (chordates)

Ensembl Genomes

http://www.ensemblgenomes.org webcite

Genome browser and annotation (nonchordates)

Gbrowse

http://flybase.net/cgi-bin/gbrowse/dmel/ webcite

Genome browser and annotation (fruit fly)

NCBI Map Viewer

http://www.ncbi.nlm.nih.gov/mapview/ webcite

Genome browser and annotation (multi-species)

NCBI Sequence Viewer

http://www.ncbi.nlm.nih.gov webcite

Genome browser and annotation (multi-species)

UCSC Browser

http://genome.ucsc.edu/ webcite

Genome browser and annotation (multi-species)

VISTA Enhancer Browser

http://enhancer.lbl.gov/ webcite

Non-coding elements (human)

1000 Genomes Browser

http://browser.1000genomes.org/ webcite

Genome browser (human, multiple individuals)

IGB

http://tinyurl.com/n83lnn webcite

Visualization tool (multiple sources)

IGV

http://www.broadinstitute.org/igv/ webcite

Visualization tool (multiple sources)

    DAS

DAS Registry

http://www.dasregistry.org/ webcite

DAS sources available

Ensembl DAS list

http://www.ensembl.org/das/dsn webcite

DAS sources available in Ensembl

    Protein and Nucleotides RefSeq

http://www.ncbi.nlm.nih.gov/RefSeq webcite

Repository of nucleic acid and protein sequences

UniProt

http://www.uniprot.org webcite

Repository of protein sequence (manually curated)

    Tools

BioMart

http://www.biomart.org webcite

Data mining tool for export of tables and sequences

EMBOSS

http://emboss.sourceforge.net/ webcite

Open source software for molecular biology

TreeBest

http://treesoft.sourceforge.net/njtree.shtml webcite

Construction and analysis of phylogenetic trees

    Regulatory Features CisRed

http://www.cisred.org webcite

Database: Regulatory sequences

DNase I Footprint

http://www.flyreg.org webcite

Database: Transcription factor binding sites (fly)

miRanda

http://www.microrna.org webcite

Database: miRNA targets (multi-species)


Major genomics resources with links to websites.

Spudich and Fern├índez-Su├írez BMC Genomics 2010 11:295   doi:10.1186/1471-2164-11-295

Open Data