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KBWS: an EMBOSS associated package for accessing bioinformatics web services.

Oshita K, Arakawa K, Tomita M - Source Code Biol Med (2011)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan. gaou@sfc.keio.ac.jp.

ABSTRACT
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 http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal).

No MeSH data available.


Related in: MedlinePlus

Sequence Logo created by example workflow. This sequence logo image is created by example workflow for generating a sequence logo image for a set of amino acid sequences of FOXP2. This workflow includes KBWS Tools (kblast, kmuscle, kweblogo), EMBOSS tool (extractalign), and other local tools (sed, uniq).
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Figure 1: Sequence Logo created by example workflow. This sequence logo image is created by example workflow for generating a sequence logo image for a set of amino acid sequences of FOXP2. This workflow includes KBWS Tools (kblast, kmuscle, kweblogo), EMBOSS tool (extractalign), and other local tools (sed, uniq).

Mentions: The following set of commands comprises a workflow for generating a sequence logo image for a set of amino acid sequences of FOXP2 [17], using BLAST web service (kblast), extracting the list of IDs (sed and uniq), aligning the sequences with MUSCLE (kmuscle), extracting a certain region from the alignment (extractalign), and generating its sequence logo (kweblogo). Output from this workflow is shown in Figure 1. The definition of "swissprot" database used in the following workflow is available at http://soap.g-language.org/kbws/embossrc.


KBWS: an EMBOSS associated package for accessing bioinformatics web services.

Oshita K, Arakawa K, Tomita M - Source Code Biol Med (2011)

Sequence Logo created by example workflow. This sequence logo image is created by example workflow for generating a sequence logo image for a set of amino acid sequences of FOXP2. This workflow includes KBWS Tools (kblast, kmuscle, kweblogo), EMBOSS tool (extractalign), and other local tools (sed, uniq).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3101651&req=5

Figure 1: Sequence Logo created by example workflow. This sequence logo image is created by example workflow for generating a sequence logo image for a set of amino acid sequences of FOXP2. This workflow includes KBWS Tools (kblast, kmuscle, kweblogo), EMBOSS tool (extractalign), and other local tools (sed, uniq).
Mentions: The following set of commands comprises a workflow for generating a sequence logo image for a set of amino acid sequences of FOXP2 [17], using BLAST web service (kblast), extracting the list of IDs (sed and uniq), aligning the sequences with MUSCLE (kmuscle), extracting a certain region from the alignment (extractalign), and generating its sequence logo (kweblogo). Output from this workflow is shown in Figure 1. The definition of "swissprot" database used in the following workflow is available at http://soap.g-language.org/kbws/embossrc.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan. gaou@sfc.keio.ac.jp.

ABSTRACT
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 http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal).

No MeSH data available.


Related in: MedlinePlus