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HMMER hmmscan (REST)

Important announcement

Please note that this tool will be phased out by 1st October 2017. A replacement is available at http://www.ebi.ac.uk/Tools/hmmer/search/phmmer Users are encouraged to start using the new tool immediately and to contact us via http://www.ebi.ac.uk/support with any queries you may have.

Description

HMMER1) 2) hmmscan searches a database of Hidden Markov Model (HMM) protein signatures with a protein sequence.

For more information see:

Important

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.

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 hmmer_hmmscan_lwp.pl LWP and XML::Simple

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

WADL

The WADL for the HMMER hmmscan (REST) service: http://www.ebi.ac.uk/Tools/services/rest/hmmer_hmmscan?wadl

Resources

parameters

List parameter names.

Request

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

Response

An XML document containing a list of parameter names.

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

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/hmmer_hmmscan/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/hmmer_hmmscan/parameterdetails/database.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/hmmer_hmmscan/run/
POST email User e-mail address. See Why do you need my e-mail address?
title An optional title for the job.
database Database to search.
cutoffOption Threshold method for search.
evalue Expectation value (E-value) threshold for reporting hits. Used when cutoffOption is set to use E-value for the threshold.
sequence Query protein sequence. The use of fasta formatted sequence is recommended.

More detailed information about each parameter, including valid values can be 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/hmmer_hmmscan/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/hmmer_hmmscan/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/hmmer_hmmscan/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) Eddy S.R. (2011)
Accelerated Profile HMM Searches.
PLoS Computational Biology 7(10):e1002195
PubMed: 22039361
DOI: 10.1371/journal.pcbi.1002195
 
services/pfa/hmmer_hmmscan_rest.txt · Last modified: 2017/07/18 18:13 by afoix
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