KBWS: an EMBOSS associated package for accessing bioinformatics web services

<jats:title>Abstract</jats:title> <jats:p>The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.g-language.org/kbws/" ext-link-type="uri">http://www.g-language.org/kbws/</jats:ext-link> and GitHub repository <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://github.com/cory-ko/KBWS" ext-link-type="uri">http://github.com/cory-ko/KBWS</jats:ext-link>. Users can utilize the SOAP services implemented in Perl directly via WSDL file at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://soap.g-language.org/kbws.wsdl" ext-link-type="uri">http://soap.g-language.org/kbws.wsdl</jats:ext-link> (RPC Encoded) and <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://soap.g-language.org/kbws_dl.wsdl" ext-link-type="uri">http://soap.g-language.org/kbws_dl.wsdl</jats:ext-link> (Document/literal).</jats:p>