Table 2.

Availability of GeneViTo input data.

Online Resources	Type of Data	Essential	URL
GenBank	Protein Table	yes	ftp://ftp.ncbi.nih.gov/genbank/genomes/
	FASTA nucleotide coding regions file	yes	ftp://ftp.ncbi.nih.gov/genbank/genomes/
	FASTA Nucleic Acid file	yes	ftp://ftp.ncbi.nih.gov/genbank/genomes/
	Cluster of Orthologous Groups (COGs)	no	http://www.ncbi.nlm.nih.gov/COG/
	Translation table	no	http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
Proteome Analysis Server (EBI)	Complete Proteome	yes	http://www.ebi.ac.uk/proteome/index.html
SwissProt			http://us.expasy.org/sprot/
WebCutter	Restriction Enzymes Sites	no	http://www.firstmarket.com/cutter/cut2.html
PRED-CLASS	Protein Structural Classification	no	http://biophysics.biol.uoa.gr/PRED-CLASS/
PRED-TMR2 and orienTM *	Prediction of TM region location and orientation	no	http://biophysics.biol.uoa.gr/PRED-TMR2/, and http://biophysics.biol.uoa.gr/orienTM/
SIGNALP	Signal Peptides	no	http://www.cbs.dtu.dk/services/SignalP/

A list of web-based resources and tools providing input data for visualization with GeneViTo. Essential data types are the minimum required data-set in order to load a Genome into GeneViTo. * PRED-TMR2 and orienTM can be executed in a single step from the orienTM web-server http://biophysics.biol.uoa.gr/orienTM/