-
-
- 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.
-
Jalview includes clients for a variety of web services for both + bioinformatic data retrieval and analysis.
-
-
- JNet
- This is a front end to the existing JNet www server - allowing single sequence or profile based prediction.
+ - 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).