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:
  • Jalview SOAP Web Services for sequence alignment and secondary structure prediction based at the University of Dundee.
  • Services for submitting IDs and sequences to external bioinformatics services such as Envision2.
  • Programs for multiple sequence alignment, made available via Java Bioinformatic Analysis Web Service (JABAWS) servers.
  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 are SOAP based services exposing protein sequence alignment and secondary structure prediction programs. These services actually run on the cluster based in the School of Life Sciences, University of Dundee, and are maintained by the Barton group.

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).

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.

Current services:

Multiple Sequence Alignment Services
• ClustalW Multiple Alignment and re-alignment
  The clustal W service remains one of the more popular Jalview features.
• Muscle Multiple Alignment
  High Quality and High Throughput multiple alignments of proteins. This method can sometimes be more accurate than ClustalW when dealing with diverse sets of sequences.
• MAFFT
  Multiple Alignment with Fast Fourier Transforms - a highly accurate and high throughput dna and amino acid alignment method, performing at least as well as ClustalW and Muscle.
• Other alignment methods are also available via JABAWS. For more information about a particular service, see the documentation available via the web services parameter dialog box.
• Secondary Structure Prediction
  • JNet
    This is a front end to the JNet www server allowing single sequence or profile based prediction.