spacer
spacer

WSWUBlast

Important

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

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

Description

WU-BLAST (Washington University Basic Local Alignment Search Tool) Version 2.0 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.

For more information about this tool see:

Web service registry entries:

Note: for new development it is recommended that the Document/literal SOAP service is used instead of the RPC/encoded SOAP service described here.

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: wswublast.exe; Source: wswublast.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: WSWUBlast.jar; Source: WSWUBlastClient.java Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in lib-1.4.zip.
Perl wublast.pl SOAP::Lite
Taverna 1.x EBI_WU-BLAST Taverna

For further details see WSWUBlast Clients.

Workflows

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

WSDL

Service API

getDatabases

Get the list of available database names for use in the inputParams structure.

Arguments: none

Returns: an array of outData objects describing the available options.

getFilters

Get the list of available low complexity sequence filter names for use in the inputParams structure.

Arguments: none

Returns: an array of outData objects describing the available options.

getMatrices

Get the list of available scoring matrix names for use in the inputParams structure.

Arguments: none

Returns: an array of outData objects describing the available options.

getPrograms

Get the list of available program names for use in the inputParams structure.

Arguments: none

Returns: an array of outData objects describing the available options.

getSensitivity

Get the list of available search sensitivity option values for use in the inputParams structure.

Arguments: none

Returns: an array of outData objects describing the available options.

getSort

Get the list of available hit sort names for use in the inputParams structure.

Arguments: none

Returns: an array of outData objects describing the available options.

getStats

Get the list of available statistical model names for use in the inputParams structure.

Arguments: none

Returns: an array of outData objects describing the available options.

getXmlFormats

Get the list of available XML format names for use in the inputParams structure.

Arguments: none

Returns: an array of outData objects describing the available options.

runWUBlast(params, content)

Submits a WU-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.

blastp(database, sequence, email)

Deprecated: use runWUBlast(params, content) instead.

Submits a blastp (protein vs. protein) search using the default parameters.

Arguments:

  • database the name of the database to search. See databases.
  • sequence the query sequence as a string.
  • email the user's e-mail address.

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

blastn(database, sequence, email)

Deprecated: use runWUBlast(params, content) instead.

Submits a blastn (nucleotide vs. nucleotide) search using the default parameters.

Arguments:

  • database the name of the database to search. See databases.
  • sequence the query sequence as a string.
  • email the user's e-mail address.

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

getOutput(jobid)

Deprecated: use poll(jobid, type) instead.

Get the text BLAST report as a string.

Arguments:

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

Returns: a string containing the BLAST output.

getXML(jobid)

Deprecated: use poll(jobid, type) instead.

Get the XML BLAST report as a string.

Arguments:

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

Returns: a string containing the BLAST XML output.

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.

doWUBlast(params, content)

Deprecated: use runWUBlast(params, content) instead.

polljob(jobid, outformat)

Deprecated: use poll(jobid, type) instead.

outData

Structure containing option descriptions for a parameter.

Attribute Type Description
name string Option value that should be passed as the parameter value.
print_name string Display name for use in user interfaces such as menus.
selected string Flag indicating if the option value is selected by default. Values: yes or no.
data_type string Database type for which this option is valid. Values: nucleotide or protein.
input_type string Input sequence type for which this option is valid. Values: nucleotide or protein.
search_type string Search type for which this option value is valid. Values: nucleotide or protein.

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. See the getPrograms() method for the available options. required
database string Database to search. See the getDatabases() method for the available options. required
sort string Sort order for hits in result. See the getSorts() method for the available options. 'pvalue'
filter string Low complexity sequence filter. See the getFilters() method for the available options. 'seg' for protein; 'dust' for nucleotide
matrix string Scoring matrix. See the getMatrices() method for the available options. 'BLOSUM62' for protein; 'Identity' for nucleotide
numal integer Maximum number of alignments in output. 50
scores integer Maximum number of scores in output. 100
topcombon integer
exp float Expectation value threshold. 10.0
echofilter boolean Include filtered input sequence in output. false
stats string Statistics. See the getStats() method for the available options. 'sump'
strand string Query search stand to use in search. Values: 'top', 'bottom', 'both' 'both'
sensitivity string Search sensitivity setting. See the getSensitivity() method for the available options. 'normal'
appxml string Generate application XML. See the getXmlFormats() method for the available options. 'no' (EBI Application XML)
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/wswublast.txt · Last modified: 2013/04/23 16:47 by hpm
spacer
spacer