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

• NCBI BLAST (REST)
• NCBI BLAST (SOAP)

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

NCBI BLAST is a sequence similarity search program. The emphasis is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of the query sequence. WU-BLAST and NCBI BLAST are distinctly different software packages, although they have a common lineage for some portions of their code, so the two services do their work differently, obtain different results and offer different features.

For more information about this tool see:

• EMBL-EBI Tools:
  • NCBI BLAST
  • NCBI BLAST Help
• NCBI:
  • NCBI BLAST Help
  • BLAST Guide

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

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: wsncbiblast.exe
• Source code: wsncbiblast.cs

Run without arguments to get a usage summary:

wsncbiblast.exe

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

Download the Java client:

• Executable: WSNCBIBlast.jar
• Source code: WSNCBIBlastClient.java

To get usage information run the client without arguments:

java -Djava.ext.dirs=lib -jar WSNCBIBlast.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: ncbiblast.pl

To get usage information run without arguments:

perl ncbiblast.pl

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 WSNCBIBlast can be found on myExperiment.