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MView (REST)

Description

MView 1) re-formats the results of a sequence database search (BLAST, FASTA, etc) or a multiple alignment (MSF, PIR, CLUSTAL, etc) adding optional HTML markup to control colouring and web page layout.

When generating a multiple sequence alignment from a sequence database search result MView uses only the sequence data which appears in the search result. As a consequence regions of the query sequence and/or the hits found which are not matched do not appear in the generated alignment, however the alignments found in the search are retained as part of the multiple alignment. This contrasts with the method used by DbClustal (DbClustal (REST) or DbClustal (SOAP)) which uses the full length sequences (query and hits) to generate the alignment.

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 mview_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 MView (REST) service: http://www.ebi.ac.uk/Tools/services/rest/mview?wadl

Resources

parameters

List parameter names.

Request

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

Response

An XML document containing a list of parameter names.

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

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/mview/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/mview/parameterdetails/outputformat.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/mview/run/
POST email User e-mail address. See Why do you need my e-mail address?
title An optional title for the job.
stype Input sequence type.
informat Input alignment or sequence similarity search result format.
outformat Output alignment format.
htmlmarkup Type of HTML mark-up used for output.
css Enable/disable use of Cascading Style Sheets (CSS) in output HTML.
pcid Basis for percent identity calculation.
alignment Show/hide alignment in output.
ruler Show/hide ruler in output.
width Width for output alignment.
coloring Basic style of colouring.
colormap Colour map.
groupmap Group map.
consensus Show/hide consensus.
concoloring Basic style of consensus colouring.
concolormap Consensus colour map.
congroupmap Consensus group map.
congaps Enable/disable counting of gaps during consensus computations.
sequence Input alignment or sequence similarity search result. For sequence similarity search jobs run on the EMBL-EBI services with supported output formats an EMBL-EBI job identifier can be used as input.

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/mview/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/mview/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/mview/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) Brown N.P., Leroy C. and Sander C. (1998)
MView: a web-compatible database search or multiple alignment viewer.
Bioinformatics 14(4):380-1
PubMed: 9632837
DOI: 10.1093/bioinformatics/14.4.380
 
services/msa/mview_rest.txt · Last modified: 2014/09/05 11:36 by uludag
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