KBWS: an EMBOSS associated package for accessing bioinformatics web services

Table 1 List of supported services

Category	Service Name	References	Tool Name
*ALIGNMENT LOCAL*	BLAST	Altschul et al., 1990	kblast
		McWilliam et al., 2009
	SSEARCH	Mackey et al., 2002	kssearch
		McWilliam et al., 2009
*ALIGNMENT MULTIPLE*	ClustalW	Larkin et al., 2007	kclustalw
		McWilliam et al., 2009
	MAFFT	Katoh et al., 2009	kmafft
	Kalign	Lassmann et al., 2006	kkalign
		McWilliam et al., 2009
	MUSCLE	Edgar, 2004	kmuscle
	T-Coffee	Notredame et al., 2000	ktcoffee
		McWilliam et al., 2009
*NUCLEIC COMPOSITION*	WebLogo	Crooks et al., 2004	kweblogo
*NUCLEIC GENE FINDING*	GeneMarkHMM	Lukashin et al., 1998	kgenemarkhmm
	GLIMMER	Delcher et al., 1999	kglimmer
	tRNAscan-SE	Lowe et al., 1997	ktrnascan_se
*PROTEIN LOCALIZATION*	PSORT	Nakai et al., 1991	kpsort
	PSORT2	Nakai et al., 1991	kpsort2
	PSORT-B	Yu et al., 2010	kpsortb
	WoLF PSORT	Horton et al., 2007	kwolfpsort
*PROTEIN MOTIFS*	Phobius	Lukas et al., 2004	kphobius
		McWilliam et al., 2009
*PROTEIN PROFILES*	dbFetch	Labarga et al., 2007	kfetchdata, kfetchbatch
		McWilliam et al., 2009
*RNA 2D STRUCTURE DISPLAY*	Centroid Fold	Sato et al., 2009	kcentroidfold
	RNAfold	Hofacker et al., 1994	krnafold
*PATHWAY MAPPING*	PathwayProjector	Kono et al., 2009	kpathwayprojector
*PHYLIP Tools*	PHYLIP	Lim et al., 1999	kclique, kcontml
			kdnacomp, kdnadist
			kdnainvar, kdnaml
			kdnamlk, kdnapars
			kdnapenny, kdollop
			kdolpenny, kfitch
			kgendist, kkitsch, kmix
			kneighbor, kpenny
			kprotdist, kprotpars
			krestml, kseqboot

The software categories are based on those used in EMBOSS. Complete listings including full references and URLs are available at our website (http://www.g-language.org/kbws/).

ISSN: 1751-0473