spacer
spacer

WSPSIBlast

Important

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

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

Description

BLAST stands for Basic Local Alignment Search Tool.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 your novel sequence. Position specific iterative BLAST (PSI-BLAST) refers to a feature of NCBI BLAST 2.0 in which a profile is automatically constructed from the first set of BLAST alignments. PSI-BLAST is similar to NCBI BLAST except that it uses position-specific scoring matrices derived during the search, this tool is used to detect distant evolutionary relationships.

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 the manual mode, for the automatic mode see the WSBlastpgp service.

For more information about 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
Perl psiblast.pl SOAP::Lite

For further details see WSPSIBlast Clients.

WSDL

Service API

runPSIBlast(params, content, preselseqcontent, checkpointcontent)

Submits a PSI-Blast job to the service.

Arguments:

  • params an instance of the inputParams data structure.
  • content data data structures describing the query sequence data.
  • preselseqcontent data structures describing the pre-selelcted sequence data.
  • checkpointcontent data structures describing the checkpoint data.

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

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
preselseqcontent file A sequence file containing pre-selected sequences for next iteration optional
checkpointcontent file A checkpoint file for next iteration optional

inputParams

A structure containing the parameters required to run the job.

Attribute Type Description Default
database string The subject database for searching required
matrix string Scoring matrix blosum62
exp real E-value (0<E⇐ 1000). Statistical significance threshold for reporting database sequence matches. 10
filter string Low complexity filter False
expmulti real PSI-Blast threshold (0<E⇐ 1000). Statistical significance threshold for selecting hits for next iteration 0.001
dropoff int Dropoff score 15
finaldropoff int Final dropoff score 25
align int number of alignments to be reported 500
scores int number of scores to be reported 500
numal int Number of alignments 500
opengap int Gap open penalty 11
extendgap int Gap extension penalty 1
checkpoint file checkpoint file for further iteration Optional
preselseq file selected sequences for next iteration Optional
async boolean Asynchronous submission 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/wspsiblast.txt · Last modified: 2013/04/23 16:45 by hpm
spacer
spacer