The IBCP have integrated several tools for protein sequence analysis with the Web services technology. These Bioinformatics Web services provide scientists and developers with programmatic access to these tools. Our Web services are build upon standards from the W3C like SOAP, WSRF and HTTP. These tools can be use remotely through a graphical and integrated SOAP client like Taverna or Triana. You can also write your own SOAP client with languages such as Python & ZSI, C/C++ gSOAP, perl SOAP::Lite or Java.
Bioinformatics Tools available
| Type of analysis | Description | Documentation | Examples of clients |
|||
|---|---|---|---|---|---|---|
| ClustalW | multiple alignment | wsdl | usage | PyZSI | Tav2 ( pict) | |
| Multalin | multiple alignment | wsdl | usage | PyZSI | Tav2 ( pict) | |
| BLAST | sequence similarity | wsdl | usage | PyZSI | Tav2 ( pict) | |
| FastA | sequence similarity | wsdl | usage | PyZSI | Tav2 ( pict) | |
| SSearch | sequence similarity | wsdl | usage | PyZSI | Tav2 ( pict) | |
| Dsc | secondary structure of protein | wsdl | usage | PyZSI | Tav2 ( pict) | |
| Gor I | secondary structure of protein | wsdl | usage | PyZSI | Tav2 ( pict) | |
| Gor III | secondary structure of protein | wsdl | usage | PyZSI | Tav2 ( pict) | |
| Gor IV | secondary structure of protein | wsdl | usage | PyZSI | Tav2 ( pict) | |
| Predator | secondary structure of protein | wsdl | usage | PyZSI | Tav2 ( pict) | |
| Simpa96 | secondary structure of protein | wsdl | usage | PyZSI | Tav2 ( pict) | |
| Protein
Secondary Consensus |
secondary structure of protein | wsdl | usage | PyZSI | Tav2 ( pict) | |
| Coils | coiled-coil regions | wsdl | usage | PyZSI | Tav2 ( pict) | |
| PcProf | physico-chemical profiles | wsdl | usage | PyZSI | Tav2 ( pict) | |
Examples of input data: one protein sequence | few protein sequences
The list of available tools described above include:
- a link to the description of the service with the WSDL standard
- a documentation of the usage of the service
- some examples of clients in Python (linked through the 'PyZSI' symbole, writen with the help of the ZSI SOAP toolkit)
- some examples of client workflow for the Taverna software (linked through the 'Tav2' symbole, for the current version 2 of this software). You can find details about the Taverna tool on the official web site : link.
Registration in repository
We have registered our services in two online repositories: the EMBRACE registry and the SEEKDA search engine. The most important advantage of such registries are to provide users with a single point of contact where they can find the services they need to analyze their data. The EMBRACE registry is also monitoring the availability of the services with some functional tests we have provided.EMBRACE registry [URL] : The IBCP services are listed at that URL.
SEEKDA search engine [URL] : You can see all our Web services on our provider's page [IBCP@SEEKDA] , or by making a search with these keywords 'provider:"ibcp.fr"'.
