CINEMA provides simple and transparent access to a variety of bioinformatics services, including automatic alignment and sequence annotation services.
Access to services is provided in a context-sensitive manner: the range of services available at an specific time will depend on the nature of the data you are working with. The "services menu" automatically updates and tailors itself to provide only those services that are useful to your current alignment, and it takes into account any specific sequences you may have selected.
To give a very simple example, automatic alignment services will only be available if you have more than one sequence in your alignment. This seems obvious, but it means that if, you only are only working with a single sequence, the services menu is not cluttered with options that are of no use to you.
This rest of this section illustrates two examples of using remote services from within CINEMA: Automatic alignment services
and Sequence annotation services.
CINEMA also provides access to sequence similarity searches, specifically BLAST which is available as part of the Find-O-Matic tool.
Note that the services list is updated "live" every time you open the services menu. Many of the actual services used are not hosted by UTOPIA and, as such, we have no control over their availability. This means that, from time-to-time, certain services may "disappear" from the services list; in such cases it is likely that these services are temporarily down. The services should re-appear in the list (and hence be accessible) when they are brought back online by their hosts.
We aim to provide continuous and reliable access to the services hosted on the UTOPIA server. However, our services have only recently become "live", and until we have a better idea of the potential demand for them we cannot guarantee that our server will always be accessible.
We maintain a page (http://utopia.cs.manchester.ac.uk/serviceinfo/) listing the services accessible via UTOPIA tools. This page shows which services are currently available and which (if any) are unavailable. If a service is unavailable, we will attempt to provide details of why, and an estimate of when the service will come back online. Please contact us if you are having difficulties accessing services.
The list of services accessible through CINEMA is, as the time of this release, quite small. However, we are continually improving the integration of services with UTOPIA and, as we do so, more and more services will become available for use from within CINEMA.
One of the most useful services you might want to use from within CINEMA is an automatic alignment service, e.g. a service that uses an algorithm such as ClustaW (http://www.ebi.ac.uk/clustalw/) or MUSCLE (http://www.drive5.com/muscle/) to perform an initial alignment of your sequences, which could then be tweaked by hand.
Using an automatic alignment service is very simple and can be performed in a single, fast, step, without leaving the Alignment View interface. To align your sequences:
- Right-click in the alignment to bring up the context menu; open up the Services... sub-menu.
- The list of currently available services will appear; you should see some entries in the list for alignment services, such as "ClustalW" and "Muscle". Choose one of these alignment services.
- When the service completes, the Alignment View will refresh to show the resulting alignment.
That's it! You can now continue to work with your alignment as normal.
An annotation service takes a sequence as input and annotates it with information obtained from a database, or as the result of running some analysis or prediction algorithm. An example of an annotation service is DSSP, which takes a protein structure (i.e. a sequence obtained from PDB) as input and annotates it with secondary structure information, assigned using the DSSP database (http://swift.cmbi.ru.nl/gv/dssp/).
To annotate a sequence using the DSSP service:
- Right-click on the sequence you wish to annotate to bring up the context menu; open up the Services... sub-menu.
- The list of currently available services will appear; Choose Annotate with secondary structure assigned using DSSP.
When the service finishes, you can see the results by using the Annotations manager.
There should be a new annotation group for the sequence, containing the secondary structure assignment made by the DSSP algorithm.
Note that this service will only work on sequences that have structure information present (e.g. sequences obtained from PDB) - if you choose a sequence without structure information then the DSSP service will not appear in the services list.