spacer
spacer

WSNCBIBlast

Important

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

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

Description

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:

Web services registry entries:

Clients

Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language Download Requirements
C# .NET Executable: wsncbiblast.exe; Source: wsncbiblast.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: WSNCBIBlast.jar; Source: WSNCBIBlastClient.java Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in lib-1.4.zip.
Perl ncbiblast.pl SOAP::Lite
Taverna 1.x EBI_NCBI_BLAST Taverna

For further details see WSNCBIBlast Clients.

Workflows

In addition to these sample clients users have submitted workflows using these services to the myExperiment workflow repository. See workflows using the WSNCBIBlast Web Service for a list.

WSDL

Service API

runNCBIBlast(params, content)

Submits a NCBI BLAST job to the service.

Arguments:

  • params an instance of the inputParams data structure.
  • content a list of data data structures describing the query sequence data.

Returns: a string containing the job ID (jobid).

getIds(jobid)

Get the entry IDs of the hits in the BLAST output.

Arguments:

  • jobid the job identifier specifying the job to get the IDs from.

Returns: a string array of entry IDs.

checkStatus(jobId)

Get the status of a job.

Arguments:

  • jobid the job identifier of the job to check status of.

Returns: a string indicating the status of the job. Current values are:

  • DONE: job has finished, and the results can then be retrieved.
  • ERROR: the job failed or no results where found
  • NOT_FOUND: the job id is no longer available (job results are deleted after 24 h)
  • PENDING: the job is in a queue waiting processing
  • RUNNING: the job is currently being processed

getResults(jobid)

Get details of the result types available.

Arguments:

  • jobid the job identifier of the job to get result types for.

Returns: an array of WSFile structures describing the available result types for the job.

poll(jobid, type)

Wait until the job has finished and get the specified type of result data.

Arguments:

  • jobid the job identifier of the job to get result from.
  • type a string specifying the type of result to retrieve. See getResults(jobid) and WSFile for details of how to obtain valid values.

Returns: a base64 encoded string containing the result data. Depending on the SOAP library and programming language used the result may be returned in decoded form.

data

Structure containing the input data for the job

Attribute Type Description Default
type string Type of content being used. Valid values are: 'sequence' and 'dbfetch' required
content string A sequence entry identifier in db:id format or a formatted sequence (fasta recommended) required

For example to specify an input sequence in Java:

Data inSeq = new Data();
inSeq.setType = "sequence";
inSeq.setContent = ">TestSequence\nASAMPLESEQ\n";

inputParams

A structure containing the parameters required to run the job.

Attribute Type Description Default
program string BLAST program to use. Valid values are: 'blastn', 'blastp', 'blastx' required
database string Database to search. See databases required
matrix string Scoring matrix to use. See matrix BLOSUM62
numal integer Maximum number of alignments to output 50
scores integer Maximum number of scores to output 100
exp float Statistical significance threshold 10
filter boolean Mask low complexity sequence false
opengap integer Gap open penalty
extendgap integer Gap extension penalty
dropoff integer Drop-off
gapalign boolean Perform optimised alignments within regions involving gaps true
match integer Reward for a nucleotide match (blastn only)
mismatch integer Penalty for a nucleotide mismatch (blastn only)
async boolean Asynchronous submission (recommended) false
email string Valid email address. See Why do you need my e-mail address? required

WSFile

Structure describing a result type. Returned by the getResults(jobid) method.

Attribute Type Description
type string Symbolic name of the result type. Used with the poll(jobid, type) method.
ext string Recommended file extension for this result type.

Contact

If you have any questions or comments, or you plan to use this service as part of a course or for a high number of submissions, please contact us EMBL-EBI Support.

 
services/archive/sss/wsncbiblast.txt · Last modified: 2013/04/23 16:44 by hpm
spacer
spacer