On Monday 28th March 2011 the WSFasta service, used by these clients, was decommissioned and replaced by the following services:

• FASTA (REST)
• FASTA (SOAP)
• FASTM (REST)
• FASTM (SOAP)

The service documentation and clients below are historical and provided solely for reference purposes.

FASTA (pronounced FAST-Aye) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison. This program achieves a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised searches for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word hits to identify potential matches before attempting the more time consuming optimised search. The trade-off between speed and sensitivity is controlled by the ktup parameter, which specifies the size of the word. Increasing the ktup decreases the number of background hits. Not every word hit is investigated but instead initially looks for segment's containing several nearby hits.

For more information see:

• EMBL-EBI Tools:
  • FASTA and SSEARCH
  • Specialist domain FASTA services:
    • ASD FASTA
    • Genomes FASTA
    • LGICdb FASTA
    • Proteomes FASTA
    • SNP FASTA
    • WGS FASTA
  • FASTA Help
• FASTA homepage

For details of the service used by these clients see WSFasta.

The Microsoft .NET runtime is already installed on most MS Windows systems. The Microsoft .NET runtime is available via Microsoft Update or as a download (see http://msdn.microsoft.com/netframework/).

For MacOS X, Linux and other non-Windows systems see Mono or DotGNU.

Download the C# client:

• Executable: wsfasta.exe
• Source code: wsfasta.cs

Run without arguments to get a usage summary:

wsfasta.exe

Download and unzip the library files lib-1.4.zip and add the jars to the Java classpath.

Download the Java client:

• Executable: WSFasta.jar
• Source code: WSFastaClient.java

To get usage information run the client without arguments:

java -Djava.ext.dirs=lib -jar WSFasta.jar

To run the Perl client you need to install SOAP::Lite. SOAP::Lite is a collection of Perl modules which provides a simple and lightweight interface to SOAP both on client and server side. This client requires SOAP::Lite version 0.60.

Download the Perl client: fasta.pl

To get usage information run without arguments:

perl fasta.pl

A number example clients are available in a range of languages:

• Ruby (tutorial)
  • Using SOAP4r: wsfasta.rb

Workflow engines such as Taverna and Triana offer a simple way of combining individual web services into complex applications.

A basic workflow showing how to use WSFasta can be found on myExperiment.