About

Keio Bioinformatics Web Service (KBWS) is an EMBASSY (EMBOSS associated software) package for accessing popular bioinformatics web services.
As an EMBOSS package, KBWS can be accessed from a number of graphical user interfaces, including EMBOSS Explorer, JEMBOSS, and wEMBOSS.



You can start using KBWS from your web browser via EMBOSS Explorer.



The latest stable release (1.0.9).

KBWS package is released under the GNU General Public License for non-commercial and education use (limited due to wsdl2h).


Publication

Oshita, K., Arakawa, K. and Tomita, M. (2011) KBWS: an EMBOSS associated package for accessing bioinformatics web services, Source Code Biol. Med., 6, 8.
Full-text PubMed

Source Code

Older versions are available at following URL : http://www.g-language.org/kbws/source/
Source code of KBWS is also freely available at GitHub repository.


Manual

README included in KBWS package is available from here.
Manuals about each tool are available from List of Supported Services section.


Database Definition

The definitions of some databases is available from here.
"embossrc" file including all databases definitions is also available at following URL : http://soap.g-language.org/kbws/embossrc


SOAP Services

Users can access the proxy server via SOAP serice directly (KBWS SOAP Service).
Detailed documentation about the SOAP service is available here.

Workflow

Using Taverna, users can incorporate KBWS SOAP Service into analysis workflow.
Sample workflow is available from myExperiment.

Add a new service

Users can add a new UNIX command-line tool acessing to SOAP web-based service based on KBWS package.
"How to add a new service" tutorial is available here.

List of Supported Services

Tool Name Category Original Service Reference Manual
kblast ALIGNMENT LOCAL BLAST Altschul et al., 1990
McWilliam et al., 2009
manual (EMBOSS Explorer)
kssearch ALIGNMENT LOCAL SSEARCH Pearson and Lipman, 1988
Pearson 1990
Mackey et al., 2002
McWilliam et al., 2009
manual (EMBOSS Explorer)
kclustalw ALIGNMENT MULTIPLE ClustalW Saitou et al., 1987
Higgins et al., 1994
Larkin et al., 2007
McWilliam et al., 2009
manual (EMBOSS Explorer)
kkalign ALIGNMENT MULTIPLE Kalign Leassmann and Erik, 2005
Leassmann and Erik, 2005
Leassmann and Erik, 2006
manual (EMBOSS Explorer)
kmafft ALIGNMENT MULTIPLE MAFFT Katoh et al., 2002
Katoh et al., 2005
Katoh et al., 2008
Katoh et al., 2009
manual (EMBOSS Explorer)
kmuscle ALIGNMENT MULTIPLE MUSCLE Edgar et al., 2004
Edgar et al., 2004
manual (EMBOSS Explorer)
ktcoffee ALIGNMENT MULTIPLE T-COFFEE Notredame et al., 2004
manual (EMBOSS Explorer)
kweblogo SEQEUCE COMPOSITION WebLogo Schneider and Stephens, 1990
Crooks et al., 2004
manual (EMBOSS Explorer)
kgenemarkhmm NUCLEIC GENE FINDING GeneMark.hmm Lukashin et al., 1998
manual (EMBOSS Explorer)
kglimmer NUCLEIC GENE FINDING GLIMMER Delcher et al., 1999
manual (EMBOSS Explorer)
ktrnascan_se NUCLEIC GENE FINDING tRNAscan-SE Lowe et al., 1997
manual (EMBOSS Explorer)
kpsort PROTEIN LOCALIZATION PSORT Nakai et al., 1991
manual (EMBOSS Explorer)
kpsort2 PROTEIN LOCALIZATION PSORT2 Horton and Nakai, 1997
manual (EMBOSS Explorer)
kpsortb PROTEIN LOCALIZATION PSORT-B Gardy et al., 2005
Gardy et al., 2003
Yu et al., 2010
manual (EMBOSS Explorer)
kwolfpsort PROTEIN LOCALIZATION WoLFPSORT Horton et al., 2006
Horton et al., 2007
manual (EMBOSS Explorer)
kphobius PROTEIN MOTIFS Phobius Kåll et al., 2004
Kåll et al., 2005
manual (EMBOSS Explorer)
kfetchbatch PROTEIN PROFILES dbFetch Labarga et al., 2007
manual (EMBOSS Explorer)
kfetchdata PROTEIN PROFILES dbFetch Labarga et al., 2007
manual (EMBOSS Explorer)
kcentroidfold RNA 2D STRUCTURE CentroidFold Hamada et al., 2009
Sato et al., 2009
manual (EMBOSS Explorer)
krnafold RNA 2D STRUCTURE RNAfold Zuker, M. and Stiegler,P (1981)
McCaskill, J.S. 1990
Hofacker,I.L et al. 1994
manual (EMBOSS Explorer)
kclique PHYLOGENY MOLECULAR SEQUENCE clique Lim et al., 1999
manual (EMBOSS Explorer)
kcontml PHYLOGENY MOLECULAR SEQUENCE contml Lim et al., 1999
manual (EMBOSS Explorer)
kdnacomp PHYLOGENY MOLECULAR SEQUENCE dnacomp Lim et al., 1999
manual (EMBOSS Explorer)
kdnadist PHYLOGENY MOLECULAR SEQUENCE dnadist Lim et al., 1999
manual (EMBOSS Explorer)
kdnainvar PHYLOGENY MOLECULAR SEQUENCE dnainvar Lim et al., 1999
manual (EMBOSS Explorer)
kdnaml PHYLOGENY MOLECULAR SEQUENCE dnaml Lim et al., 1999
manual (EMBOSS Explorer)
kdnamlk PHYLOGENY MOLECULAR SEQUENCE dnamlk Lim et al., 1999
manual (EMBOSS Explorer)
kdnapars PHYLOGENY MOLECULAR SEQUENCE dnapars Lim et al., 1999
manual (EMBOSS Explorer)
kdnapenny PHYLOGENY MOLECULAR SEQUENCE dnapenny Lim et al., 1999
manual (EMBOSS Explorer)
kdollop PHYLOGENY MOLECULAR SEQUENCE dollop Lim et al., 1999
manual (EMBOSS Explorer)
kdollpeny PHYLOGENY MOLECULAR SEQUENCE dollpeny Lim et al., 1999
manual (EMBOSS Explorer)
kfitch PHYLOGENY MOLECULAR SEQUENCE fitch Lim et al., 1999
manual (EMBOSS Explorer)
kgendist PHYLOGENY MOLECULAR SEQUENCE gendist Lim et al., 1999
manual (EMBOSS Explorer)
kkitsch PHYLOGENY MOLECULAR SEQUENCE kitsch Lim et al., 1999
manual (EMBOSS Explorer)
kmix PHYLOGENY MOLECULAR SEQUENCE mix Lim et al., 1999
manual (EMBOSS Explorer)
kneighbor PHYLOGENY MOLECULAR SEQUENCE neighbor Lim et al., 1999
manual (EMBOSS Explorer)
kpenny PHYLOGENY MOLECULAR SEQUENCE penny Lim et al., 1999
manual (EMBOSS Explorer)
kprotdist PHYLOGENY MOLECULAR SEQUENCE protdist Lim et al., 1999
manual (EMBOSS Explorer)
kprotpars PHYLOGENY MOLECULAR SEQUENCE protpars Lim et al., 1999
manual (EMBOSS Explorer)
krestml PHYLOGENY MOLECULAR SEQUENCE restml Lim et al., 1999
manual (EMBOSS Explorer)
kseqboot PHYLOGENY MOLECULAR SEQUENCE seqboot Lim et al., 1999
manual (EMBOSS Explorer)
kpathwayprojector MAPPING TO PATHWAY MAP Pathway Projector Kono et al., 2009
manual (EMBOSS Explorer)