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WSBlastpgp

Important

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

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

Description

Position Specific Iterative BLAST (PSI-BLAST) performs an iterative sequence similarity search which can detect more distant evolutionary relationships.

Pattern Hit Initiated BLAST (PHI-BLAST) treats multiple occurrences of a defined pattern within the query sequence as independent sequences.

These tools are only available for database protein searches.

The iterative strategy of PSI-BLAST can be run in two ways:

  1. Manual: at each iteration the list of hits found is returned and the hits used to generate the profile the next iteration are selected and submitted to perform the nest iteration.
  2. Automatic: the set of hits used to construct the profile is automatically selected based on an E-value threshold. For this mode the search will stop either when the iterations converge (i.e. the same hits are used to build the profile in each iteration) or when a specified maximum number of iterations is reached.

This service provides only the automatic mode. To use the manual mode see the WSPSIBlast, PSI-BLAST (SOAP) or PSI-BLAST (REST) services.

For more information on this tool see:

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

For further details see WSBlastpgp Clients.

Workflows

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

WSDL

Service API

runBlastpgp(params, content)

Submits a PSI-BLAST/PHI-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 Values Default
type string sequence, dbfetch required
content string db:id identifier or formatted sequence 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 Values Default
mode string 'PSI-Blast' or 'PHI-Blast' required
database string see databases required
matrix string scoring matrix name BLOSUM62
exp float 1.0e-200 < exp < 1000 10.0
expmulti float 0.0001 < expmulti < 1000 0.002
filter string T (true) or F (false) F
align int 0 (pairwise), 1 (M/S identities), 2 (M/S non-identities), 3 (Flat identities), 4 (Flat non-identities) 0
opengap int 11
extendgap int 1
gapalign string not used
dropoff int 15
finaldropoff int 25
maxpasses int 3
scores int 500
startregion int whole sequence
endregion int whole sequence
sensitivity string not used
appxml string no (text) or yes (XML) no
usagemode string blastpgp, patseedp or seedp blastpgp
pattern string
async boolean true or false 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/wsblastpgp.txt · Last modified: 2013/04/23 16:41 by hpm
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