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PSI-BLAST (REST)

Description

Position Specific Iterative BLAST (PSI-BLAST) 1) refers to a feature of NCBI BLAST 2.0 in which a position-specific scoring matrix (PSSM) profile is constructed from set of BLAST alignments. The PSSM is then used to search the database in subsequent iterations allowing the detection of distant evolutionary relationships. This can be combined with the Pattern Hit Initiated BLAST (PHI-BLAST) mode to constrain the PSSM using a ProSite pattern to define the region(s) to be used when building the PSSM.

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 psiblast_lwp.pl LWP

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/psiblast/parameters/
Parameters none

Response

An XML document containing a list of parameter names.

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

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/psiblast/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/psiblast/parameterdetails/matrix.

run

Submit a job with the specified parameters.

Please note that a submission is required for each PSI-BLAST iteration to be performed. The initial submission is equivalent to a blastp using NCBI BLAST (NCBI BLAST (REST) or NCBI BLAST (SOAP)), but provides a list of hit identifiers for input to the next iteration. The second submission uses the hit identifier list, provided either via the selectedHits parameter or by reference to the previous iteration job identifier (previousjobid) to construct the PSSM to be used for the search. The result of the second submission provides a list of hit identifiers and a checkpoint file, containing the PSSM, for input to the next iteration. Subsequent submissions use the hit identifier list and the checkpoint file, passed via the selectedHits and cpfile parameters or by reference to the previous iteration job identifier (previousjobid), to perform the next iterations of the search and return an updated a list of hit identifiers and a checkpoint file for use as input to the next iteration.

Request

Due to the cpfile parameter, required by the third and subsequent iterations, being a binary data file, the submission for these iterations should use multipart/form-data encoding for the POST instead of application/x-www-form-urlencoded encoding.

URL http://www.ebi.ac.uk/Tools/services/rest/psiblast/run/
POST email User e-mail address. See Why do you need my e-mail address?
title an optional title for the job.
matrix Scoring matrix to be used in the search.
gapopen Penalty for the initiation of a gap.
gapext Penalty for each base/residue in a gap.
expthr Search E-value threshold.
psithr E-value threshold for inclusion into PSSM.
scores Maximum number of scores displayed in the output.
alignments Maximum number of alignments displayed in the output.
alignView Alignment view.
dropoff Drop-off score for halting extension of the alignment.
finaldropoff Drop-off score for halting extension of the final gapped alignment.
filter Low complexity sequence filter.
seqrange Range defining the region of the query sequence to use in the search.
sequence Query sequence. The use of fasta formatted sequence is recommended.
database List of database names for search.
previousjobid Previous iteration's job identifier.
selectedHits Identifiers of hits to include in the PSSM.
cpfile PSI-BLAST checkpoint file from previous iteration.

More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.

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/psiblast/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/psiblast/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/psiblast/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) Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W. and Lipman D.J. (1997)
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Res. 25(17):3389-402.
PubMed: 9254694
DOI: 10.1093/nar/25.17.3389
 
services/sss/psiblast_rest.txt · Last modified: 2013/10/09 14:06 by hpm
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