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WU-BLAST (REST)

Description

WU-BLAST (Washington University Basic Local Alignment Search Tool) Version 2.0 1) is used to compare a sequence with those contained in nucleotide and protein databases by aligning the sequence with previously characterized genes. The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of this novel sequence. Regions of similarity detected via this type of alignment tool can be either local, where the region of similarity is based in 1 location, or global, where regions of similarity can be detected across otherwise unrelated genetic code.

WU-BLAST and NCBI BLAST are distinctly different software packages, although they have a common lineage for some portions of their code, so the services do their work differently, obtain different results and offer different features.

For more information see:

Web service registry entries:

Important

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 30 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.

Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the EMBL-EBI's Terms of Use.

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
Perl wublast_lwp.pl LWP and XML::Simple

For further details of these tool-kits and workflow platforms see our Guide to Web Services.

Resources

parameters

List parameter names.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/wublast/parameters/
Parameters none

Response

An XML document containing a list of parameter names.

For example: http://www.ebi.ac.uk/Tools/services/rest/wublast/parameters/

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/wublast/parameterdetails/$parameterId
Parameters $parameterId: the name of the parameter

Response

An XML document providing details about the parameter.

For example: http://www.ebi.ac.uk/Tools/services/rest/wublast/parameterdetails/program.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/wublast/run/
POST email User e-mail address (Why do you need my e-mail address?).
title An optional title for the job.
program BLAST program to use to perform the search.
matrix Scoring matrix to be used in the search.
alignments Maximum number of alignments displayed in the output.
scores Maximum number of scores displayed in the output.
exp E-value threshold.
filter Low complexity sequence filter to process the query sequence before performing the search.
align Alignment format to use in output.
stats Statistical model to use.
sensitivity Search sensitivity.
topcombon Consistent sets of HSPs to be reported.
viewfilter Display filtered sequence in output.
strand Both, upper or lower strand of a DNA/RNA query used for search.
sort Sort order for reporting hits.
stype Query sequence type. One of: dna, rna or protein.
sequence Query sequence. The use of fasta formatted sequence is recommended.
database List of database names for search.

More detailed information about each parameter, including valid values can be found in the WU-BLAST help pages or obtained using the parameterdetails resource.

Response

A plain text document containing the job identifier.

status

Get the status of a submitted job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/wublast/status/$jobId
Parameters $jobId: job identifier

Response

A plain text document containing the job status.

The values for the status are:

  • RUNNING: the job is currently being processed.
  • FINISHED: job has finished, and the results can then be retrieved.
  • ERROR: an error occurred attempting to get the job status.
  • FAILURE: the job failed.
  • NOT_FOUND: the job cannot be found.

Further details can be found in Synchronous and Asynchronous Access: JDispatcher.

resulttypes

Get available result types for a finished job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/wublast/resulttypes/$jobId
Parameters $jobId: job identifier

Response

An XML document detailing the available result types.

result

Get the job result of the specified type.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/wublast/result/$jobId/$resultType
Parameters $jobId: job identifier
$resultType: type of result to retrieve. See resulttypes.

Response

A document containing the result in the requested format. The MIME type of the returned document is set according to the format.

1) Lopez R., Silventoinen V., Robinson S., Kibria A. and Gish W. (2003)
WU-Blast2 server at the European Bioinformatics Institute.
Nucleic Acids Res. 31(13):3795-8
PubMed: 12824421
DOI: 10.1093/nar/gkg573
 
services/sss/wu_blast_rest.txt · Last modified: 2013/10/09 14:07 by hpm
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