Web services

Jalview includes clients for a variety of web services for both bioinformatic data retrieval and analysis.

• The Sequence Fetcher utilises web services for sequence, alignment and structure retrieval provided by the European Bioinformatics Institute (EBI) and Distributed Annotation System servers that are capable of serving sequences.
• The DAS Feature Fetcher enables the retrieval and visualization of features from DAS annotation sources
• The Database Reference Fetcher transfers database references from records available from DAS or the public sequence databases.
• The Web Services menu in each alignment window also provides access to the following:
  • Programs for multiple sequence alignment, made available via Java Bioinformatic Analysis Web Service (JABAWS) servers.
  • Jalview SOAP Web Services for secondary structure prediction based at the University of Dundee.
  • Services for alignment analysis, such as Multi-Harmony.
  • Services for submitting IDs and sequences to external bioinformatics services such as Envision2 (see below).

  Web Service Dialog Box

  

  This dialog box is displayed when a web service job is submitted. It gives the name of the service and any method citation information, and monitors the progress of the calculation. The cancel button will permanently cancel the job, but this is only possible for some services.

  The Web Services Preference panel controls the display and appearance of the submission and analysis services in the Web Services menu.
• If Jalview encounters problems accessing any services, it may display a warning dialog box (this can be turned off using the web services preferences tab).

More about Jalview's Web Services
Jalview's distributed computations utilise SOAP and REST web services exposing sequence alignment, analysis, and secondary structure prediction programs. Originally, Jalview 2's services were maintained by the Barton group at the University of Dundee, and ran programs on the Life Sciences High-performace Computing Cluster. With the advent of JABAWS, however, it is possible for anyone to host Jalview web services.

Envision2 Services

Since version 2.5, Jalview has included a client to enable the user to submit one or more sequences or sequence IDs to analysis workflows provided by the EnVision2 web application. This allows Jalview users to easily access the EnCore network of databases and analysis services developed by ENFIN (www.enfin.org).