Table 3:

List of commonly used available resources for functional analysis (other than homology-, motif- and context-based) that can be performed on metagenomic data sets

Type of prediction	Resource name	URL
Carbohydrate-active enzymes	CAZy	http://www.cazy.org/
Glycosyl hydrolases	GAS	http://csbl.bmb.uga.edu/∼ffzhou/GASdb/
Protein localization	PSORT	http://psort.hgc.jp/
	Cell-PLoc	http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc/
	CELLO	http://cello.life.nctu.edu.tw/
	PA-SUB	http://webdocs.cs.ualberta.ca/∼bioinfo/PA/Sub/index.html
Membrane proteins	DAS	http://www.sbc.su.se/∼miklos/DAS/
	HMMTOP	http://www.enzim.hu/hmmtop/html/submit.html
	HMM-TM	http://bioinformatics.biol.uoa.gr/HMM-TM/index.jsp
	TMB-Comp	http://bmbpcu36.leeds.ac.uk/∼andy/betaBarrel/TMB_Hunt_2/TMB_Comp.cgi
Lipoproteins	DOLOP	http://www.mrc-lmb.cam.ac.uk/genomes/dolop/dolop.htm
	LIPO	http://services.cbu.uib.no/tools/lipo
	SignalP	http://www.cbs.dtu.dk/services/SignalP/
	LipoP	http://www.cbs.dtu.dk/services/LipoP/
	PRED-LIPO	http://bioinformatics.biol.uoa.gr/PRED-LIPO/input.jsp
Secretory proteins (signal peptide Type I)	Tatfind	http://signalfind.org/tatfind.html
	TatP	http://www.cbs.dtu.dk/services/TatP/
	SignalP	http://www.cbs.dtu.dk/services/SignalP/
	PrediSi	http://www.predisi.de/index.html
Adhesins	SPAAN	Sachdeva et al. 2004 [75]
Transporters	TansportTP	http://bioinfo3.noble.org/transporter/
	TransAAP	http://www.membranetransport.org/transaap/TransAAP_login.html
	TCDB	http://www.tcdb.org/
Insertion sequences	ISsaga	http://issaga.biotoul.fr/ISsaga/issaga_index.php
CRISPRs	PILER	http://www.drive5.com/pilercr/
	CRISPRfinder	http://crispr.u-psud.fr/Server/
Repeats	Tandem Repeats Finder	http://tandem.bu.edu/trf/trf.html
	EMBOSS	http://emboss.sourceforge.net/
Virulence factors	VFDB	http://www.mgc.ac.cn/VFs/
	MvirDB	http://predictioncenter.llnl.gov/