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Biological Data Centres

  1. Phillip Stafford,
  2. HoJoon Lee

Published Online: 15 JAN 2010

DOI: 10.1002/9780470015902.a0003026.pub2

eLS

eLS

How to Cite

Stafford, P. and Lee, H. 2010. Biological Data Centres. eLS. .

Author Information

  1. Arizona State University, Tempe, Arizona, USA

Publication History

  1. Published Online: 15 JAN 2010
Table 1. Sizes of completed vertebrates genomes
MammalHomo sapiense (human)3107 million basesApproximately 24 119 genesKEGG
MammalEquus caballus (horse)2484 million basesApproximately 17 619KEGG
MammalOrnithorhynchidae (Platypus)1996 million basesApproximately 16 387 genesKEGG
MammalFelis catus (cat)4045 million basesApproximately 20 000 
MammalRattus norvegicus (rat)2834 million basesApproximately 26 142 genesKEGG
MammalMacaca mulatta (Rhesus macaque)2864 million basesApproximately 23 965KEGG
MammalPan troglodytes (chimpanzee)3350 million basesApproximately 25 184 genesKEGG
MammalCallithrix jacchus (marmoset)3030 million basesNo estimation yet 
MammalPongo pygmaeus abelii (orangutan)3446 million basesApproximately 12 728Ensembl
MammalMus musculus (mouse)2725 million basesApproximately 29 452 genesKEGG
MammalCavia porcellus (guinea pig)2723 million basesApproximately 14 143 genesEnsembl
MammalCanis lupus familiaris (dog)2531 million basesApproximately 19 807 geneKEGG
MammalBos taurus (cow)2917 million basesApproximately 22 334 genesKEGG
MammalMonodelphis domestica (opossum)3605 million basesApproximately 19 114KEGG
VertebratePetromyzon marinus (lamprey)1027 million basesNo estimation yet 
VertebrateGallus gallus (chicken)1100 million basesApproximately 18 118KEGG
VertebrateAnolis carolinensis (lizard)1781 million basesApproximately 12 043Ensembl
VertebrateGasterosteus aculeatus (stickleback)463 million basesApproximately 14 881Ensembl
VertebrateTaeniopygia guttata (zebra finch)1233 million bases1706Ensembl
VertebrateXenopus tropicalis (X. tropicalis)1513 million bases8540KEGG
VertebrateDanio rerio (zebrafish)1440 million bases27 485KEGG
VertebrateTetraodon nigroviridis (tetraodon)402 million bases27 918KEGG
VertebrateTakifugu rubripes (fugu)400 million bases22 041KEGG
VertebrateOryzias latipes (medaka)869 million bases25 084KEGG
Table 3. Bioinformatics tools websites
DescriptionSiteURL
Sequence alignmentBLASThttp://blast.ncbi.nlm.nih.gov/Blast.cgi
 ClustalW2http://www.ebi.ac.uk/Tools/clustalw2/index.html
Sequence alignment with genomeBLAThttp://genome.ucsc.edu/cgi-bin/hgBlat
Motif searchMEMEhttp://meme.sdsc.edu/meme4_1
 Prositehttp://ca.expasy.org/prosite/
Primer designPrimer3http://frodo.wi.mit.edu/
PhylogeneticsPhylogenetic programhttp://evolution.genetics.washington.edu/phylip/software.html
MHC bindingRankpephttp://bio.dfci.harvard.edu/Tools/rankpep.html
 Syfpeithihttp://www.syfpeithi.de
Genome browserUCSC genome browserhttp://genome.ucsc.edu/cgi-bin/hgGateway