External links of interest

• Institutions
• Genome browsers
• Genome databases
• Protein databases
• Homology Search
• Sequence alignment
• Motif finding
• Regulatory tools
• Gene prediction
• Regulatory databases 
• Structural biology
• Ontologies and phylogenies
• Bioinformatics

Institutions:
	EBI	www.ebi.ac.uk
	EMBL:	www.embl.org/
	NCBI:	www.ncbi.nlm.nih.gov/
	NIH:	www.nih.gov/
	NHGRI:	www.genome.gov/
	DOE genomics:	genomics.energy.gov/
	SANGER institute:	www.sanger.ac.uk/
	Janelia Farm:	www.hhmi.org/janelia/
	JCVI (J. Craig Venter Institute)	www.jcvi.org/
Genome browsers:
	Ensembl:	www.ensembl.org/
	UCSC genome browser:	genome.ucsc.edu/
	NCBI human genome:	www.ncbi.nlm.nih.gov/projects/genome/guide/human/
	FlyBase:	flybase.bio.indiana.edu/
	GMOD (Generic Model Organism Database):	www.gmod.org/
Genome databases:
	GENBANK:	www.ncbi.nlm.nih.gov/Genbank/index.html
	REFSEQ:	www.ncbi.nlm.nih.gov/RefSeq/
	EMBL:	www.ebi.ac.uk/embl/
	UNIGENE:	www.ncbi.nlm.nih.gov/UniGene/
	KEGG (Kyoto Encyclopedia of Genes and Genomes):	www.genome.jp/kegg/
	GeneCards:	www.genecards.org/
	HapMap:	www.hapmap.org/
	dbSNP:	www.ncbi.nlm.nih.gov/projects/SNP/
	OMIM (Online Mendelian Inheritance in Man):	www.ncbi.nlm.nih.gov/sites/entrez?db=omim
	NCBI Trace Archive:	www.ncbi.nlm.nih.gov/Traces/trace.cgi?
	Ensembl Trace Server:	trace.ensembl.org/
Protein databases:
	SWISS-PROT:	www.expasy.ch/sprot/
	INTERPRO:	www.ebi.ac.uk/interpro/
	UNIPROT:	beta.uniprot.org/
	PIR:	pir.georgetown.edu/
	PeptideAtlas:	www.peptideatlas.org/
Homology Search:
	NCBI BLAST:	www.ncbi.nlm.nih.gov/blast/
	WU-BLAST	blast.wustl.edu/
	Bl2seq:	www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi
	BLAT:	genome.ucsc.edu/cgi-bin/hgBlat?command=start
Sequence alignment:
	Clustalw:	www.ebi.ac.uk/Tools/clustalw2/
	T-coffee:	www.tcoffee.org/
	genewise:	www.ebi.ac.uk/Wise2/
	Boxshade:	www.ch.embnet.org/software/BOX_form.html
	MLAGAN:	lagan.stanford.edu/lagan_web/index.shtml
	MAVID	baboon.math.berkeley.edu/mavid/
	vista:	pipeline.lbl.gov/cgi-bin/gateway2
	pipmaker:	pipmaker.bx.psu.edu/pipmaker/
	gff2aplot:	genome.imim.es/software/gfftools/GFF2APLOT.html
Motif finding:
	Meme:	meme.sdsc.edu/meme/intro.html
	Muscle:	www.drive5.com/muscle/
	Footprinter:	genome.cs.mcgill.ca/cgi-bin/FootPrinter3.0/FootPrinterInput2.pl
Regulatory tools:
	TF-map alignment:	genome.imim.es/software/meta/index.html
	Phylofoot:	www.phylofoot.org/
	TESS:	www.cbil.upenn.edu/cgi-bin/tess/tess
Gene prediction:
	geneid:	genome.imim.es/software/geneid/
	genscan:	genes.mit.edu/GENSCAN.html
	fgenesh:	www.softberry.com/
	genemark:	exon.gatech.edu/GeneMark/
	twinscan/Nscan:	mblab.wustl.edu/nscan
	sgp2:	genome.imim.es/software/sgp2/
	augustus:	augustus.gobics.de/
	gff2ps:	genome.imim.es/software/gfftools/GFF2PS.html
Regulatory databases:
	TRANSFAC:	www.gene-regulation.com/pub/databases.html
	JASPAR:	jaspar.genereg.net/
	OREGANNO:	www.oreganno.org
	PAZAR:	www.pazar.info/
	ABS:	genome.imim.es/datasets/abs2005/index.html
Structural biology:
	PROSITE:	www.expasy.ch/prosite/
	PFAM:	pfam.sanger.ac.uk/
	PDB:	www.rcsb.org/pdb/
	SCOP:	iris.physics.iisc.ernet.in/scop/
	CATH:	www.cathdb.info/latest/index.html
	RASMOL:	www.umass.edu/microbio/rasmol/
	MOLMOL:	hugin.ethz.ch/wuthrich/software/molmol/
	Swiss-model:	swissmodel.expasy.org//SWISS-MODEL.html
	PHYRE:	www.sbg.bio.ic.ac.uk/phyre/
	NAD:	ndbserver.rutgers.edu/
	NDB:	http://ndbserver.rutgers.edu/
	CCDC:	www.ccdc.cam.ac.uk
Ontologies and phylogenies:
	GO:	www.geneontology.org/
	OBO:	www.obofoundry.org/
	Tree of Life:	tolweb.org/tree/phylogeny.html
Bionformatics:
	EMBOSS:	emboss.sourceforge.net/
	BioPerl:	www.bioperl.org/
	Bioinformatics Wiki:	wikiomics.org/wiki/Main_Page
	Bioinformatics.Org:	www.bioinformatics.org/
	DMOZ Open Source Repository:	www.dmoz.org/Science/Biology/Bioinformatics/Software/
	INB (Spanish Bioinformatics Institute):	www.inab.org/
	XGP (Xarxa de Genòmica i Proteòmica):	xgp.uab.es/xgp/
	BSC (Barcelona Supercomputing Center):	www.bsc.es/