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services:archive:so:wsemboss [2012/11/30 15:22]
services:archive:so:wsemboss [2013/04/23 16:35] (current)
hpm (172.22.68.212)
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 +====== WSEmboss ======
 +
 +===== Important =====
 +
 +The WSEmboss service was **decommissioned** on Wednesday 17th April 2013. For alternative EMBOSS services please see the [[..:soaplab:overview|Soaplab]] page or the program specific services described below.
 +
 +We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 25 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.
 +
 +Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the [[http://www.ebi.ac.uk/Information/termsofuse.html|EMBL-EBI's Terms of Use]].
 +
 +===== Description =====
 +
 +EMBOSS (European Molecular Biology Open Software Suite) ((Rice P., Longden I. and Bleasby A. (2000)\\
 +**EMBOSS: The European Molecular Biology Open Software Suite.**\\
 +Trends Genet. 16(6)276-277\\
 +PubMed: [[http://europepmc.org/abstract/MED/10827456|10827456]]\\
 +DOI: [[http://dx.doi.org/10.1016/S0168-9525(00)02024-2|10.1016/S0168-9525(00)02024-2]]\\
 +)) ((http://emboss.open-bio.org/)) is a free Open Source software analysis package specially developed for the needs of the molecular biology user community.
 +
 +The software automatically copes with data in a variety of formats and allows transparent retrieval of sequence data from the web. Since extensive libraries are provided with the package providing a platform to allow scientists to develop and release software in the true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
 +
 +For more information see:
 +  * [[http://emboss.open-bio.org/|EMBOSS homepage]]
 +  * [[http://en.wikipedia.org/wiki/EMBOSS|Wikipedia]]
 +
 +Web service registry entries:
 +  * [[http://www.biocatalogue.org/services/1327|BioCatalogue]]
 +  * [[http://webservices.seekda.com/providers/ebi.ac.uk/WSEmbossService|seekda!]]
 +
 +For a selection of EMBOSS tools, separate services are available, for example:
 +  * Pairwise Sequence Alignment:
 +    * [[:services:psa:EMBOSS matcher (REST)]]
 +    * [[:services:psa:EMBOSS matcher (SOAP)]]
 +    * [[:services:psa:EMBOSS needle (REST)]]
 +    * [[:services:psa:EMBOSS needle (SOAP)]]
 +    * [[:services:psa:EMBOSS stretcher (REST)]]
 +    * [[:services:psa:EMBOSS stretcher (SOAP)]]
 +    * [[:services:psa:EMBOSS water (REST)]]
 +    * [[:services:psa:EMBOSS water (SOAP)]]
 +  * Sequence Format Conversion:
 +    * [[:services:sfc:EMBOSS seqret (REST)]]
 +    * [[:services:sfc:EMBOSS seqret (SOAP)]]
 +  * Sequence Statistics:
 +    * [[:services:seqstats:EMBOSS cpgplot (REST)]]
 +    * [[:services:seqstats:EMBOSS cpgplot (SOAP)]]
 +    * [[:services:seqstats:EMBOSS isochore (REST)]]
 +    * [[:services:seqstats:EMBOSS isochore (SOAP)]]
 +    * [[:services:seqstats:EMBOSS newcpgreport (REST)]]
 +    * [[:services:seqstats:EMBOSS newcpgreport (SOAP)]]
 +    * [[:services:seqstats:EMBOSS pepinfo (REST)]]
 +    * [[:services:seqstats:EMBOSS pepinfo (SOAP)]]
 +    * [[:services:seqstats:EMBOSS pepstats (REST)]]
 +    * [[:services:seqstats:EMBOSS pepstats (SOAP)]]
 +    * [[:services:seqstats:EMBOSS pepwindow (REST)]]
 +    * [[:services:seqstats:EMBOSS pepwindow (SOAP)]]
 +  * Sequence Translation:
 +    * [[:services:st:EMBOSS backtranambig (REST)]]
 +    * [[:services:st:EMBOSS backtranambig (SOAP)]]
 +    * [[:services:st:EMBOSS backtranseq (REST)]]
 +    * [[:services:st:EMBOSS backtranseq (SOAP)]]
 +    * [[:services:st:EMBOSS sixpack (REST)]]
 +    * [[:services:st:EMBOSS sixpack (SOAP)]]
 +    * [[:services:st:EMBOSS transeq (REST)]]
 +    * [[:services:st:EMBOSS transeq (SOAP)]]
 +
 +There are many other sites providing access to the EMBOSS tools, for example see:
 +  * [[http://galaxyproject.org/|The Galaxy Project]]
 +  * [[https://projets.pasteur.fr/projects/mobyle/wiki/Mobyle_Public_Servers|Mobyle Public Servers]]
 +
 +===== Clients =====
 +
 +Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
 +
 +^ Language ^ Download ^ Requirements ^
 +^ Java | Executable jar: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/bin/WSEmboss.jar|WSEmboss.jar]]''; Source: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/src/uk/ac/ebi/webservices/WSEmbossClient.java|WSEmbossClient.java]]'' | [[http://ws.apache.org/axis/|Axis 1.4]]; All dependencies, including [[http://ws.apache.org/axis/|Axis 1.4]] and [[http://commons.apache.org/cli/|Commons-CLI]], are available in ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/lib-1.4.zip|lib-1.4.zip]]''. |
 +^ Perl | ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/perl/soaplite/emboss.pl|emboss.pl]]'' | [[http://search.cpan.org/perldoc?SOAP::Lite|SOAP::Lite]] |
 +
 +For further details see [[.:WSEmboss Clients]].
 +
 +===== WSDL =====
 +
 +http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl
 +
 +===== Contact =====
 +
 +If you have any questions or comments or you plan to use this service as part of a course or for a high number of submissions, please contact us [[http://www.ebi.ac.uk/support/index.php?query=WebServices|EMBL-EBI Support]].
 
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