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EBIEMBL-EBI Web Servicesservicessssfastm_soap
Table of Contents

FASTM (SOAP)

Description

The FASTA (pronounced FAST-Aye) suite of programs includes three specialist programs for searching sequence databases with a set of short fragments 1), as may be obtained from protein mass spectrometry or Edman protein sequencing:

  • FASTF - Compares an ordered peptide mixture, as would be obtained by Edman degradation of a CNBr cleavage of a protein, against a protein database.
  • FASTM - Compares an ordered set of peptides to a protein sequence database or an ordered set of oligonucleotides to a nucleotide sequence database.
  • FASTS - Compares a set of short peptide fragments, as would be obtained from mass spectrometry analysis of a protein, against a protein database.

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 25 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
C# .NET Executable: FastmCliClient.exe; Source: AbstractWsClient.cs, FastmClient.cs, FastmCliClient.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: Fastm_Axis1.jar; Source: AbstractWsToolClient.java, FastmClient.java Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in lib-1.4.zip.
Perl fastm_soaplite.pl SOAP::Lite

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

WSDL

The WSDL for the FASTM SOAP service: http://www.ebi.ac.uk/Tools/services/soap/fastm?wsdl

Operations

getParameters()

Get a list of the parameter names.

Arguments: none

Returns: a list of strings giving the names of the parameters.

getParameterDetails(parameterId)

Get details of a specific parameter.

Arguments:

  • parameterId: identifier/name of the parameter to fetch details of. Required.

Returns: a wsParameterDetails describing the parameter and its values.

run(email, title, params)

Submit a job to the service.

Arguments:

Returns: a string containing the job identifier (jobId).

getStatus(jobId)

Get the status of a submitted job.

Arguments:

  • jobId: job identifier. Required.

Returns: a string containing the 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.

getResultTypes(jobId)

Get the available result types for a finished job.

Arguments:

  • jobId: job identifier. Required.

Returns: a list of wsResultType data structures describing the available result types.

getResult(jobId, type, parameters)

Get the result of a job of the specified type.

Arguments:

  • jobId: job identifier. Required.
  • type: string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types. Required.
  • parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types.

Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.

Data Types

InputParameters

The input parameters for the job:

Attribute Type Description
program string FASTA suite program to use for search: fastf, fastm or fasts. Required.
stype string Query sequence type. One of: dna, protein or rna. Required.
matrix string Scoring matrix to be used in for a protein search.
match_scores string Match/missmatch scores to be used for a nucleotide search.
gapopen int Score for the initiation of a gap.
gapext int Score for each base/residue in a gap.
expupperlim double Upper E-value threshold.
explowlim double Lower E-value threshold.
strand string Nucleotide sequence strand to use for search. One of: both, top or bottom.
hist boolean Display histogram.
scores int Maximum number of scores displayed in the output.
alignments int Maximum number of alignments displayed in the output.
scoreformat string Format for scores table in FASTA output.
stats string Statistical model to use.
seqrange string Region of the query sequence to use for the search. Default: whole sequence.
dbrange string Range of sequence lengths in search database to include in search. Default: all sequences.
filter string Low complexity sequence filter to process the query sequence before performing the search.
sequence string Query set of sequence fragments. A variation of the fasta sequence format, where the fragments are separated by commas, must be used (see below). Required.
database list List of database names for search. Required.
ktup int Word size to use for sequence comparisons.

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

Note: the query set of fragment sequences must be formatted using a variation of the fasta sequence format where the individual sequence fragments each begin on a new line and are separated by commas, for example: 

>Seq_2
MKWVTFIS,
MADCCEKQ,
MREKVLAS,
MPCTEDYL,
MENFVAFV

wsParameterDetails

Descriptive information about a tool parameter. Returned by getParameterDetails(parameterId).

Attribute Type Description
name string Name of the parameter.
description string Description of the parameter, suitable for use in option help interfaces.
type string Data type of the parameter.
values list of wsParameterValue Optional list of valid values for the option.

wsParameterValue

Description of a tool parameter value. Used in wsParameterDetails.

Attribute Type Description
label string Display name of the value, for use in interfaces.
value string String representation of the value to be passed to the tool parameter.
defaultValue boolean Flag indicating if this value is the default.
properties list of wsProperty Optional list of key/value pairs providing further information.

wsProperty

Properties of a tool parameter value. Used in wsParameterValue.

Attribute Type Description
key string Name of the property.
value string Value of the property.

wsRawOutputParameter

Additional parameters passed when requesting a result. See getResult(jobId, type, parameters).

Attribute Type Description
name string Name of the parameter.
value list of string Value for the parameter.

wsResultType

Description of a result type. Returned by getResultTypes(jobId).

Attribute Type Description
identifier string Identifier for the result type. Passed as type to getResult(jobId, type, parameters).
label string Display name for use in user interfaces.
description string Description of the result type, for use in help interfaces.
mediaType string MIME type of the returned data.
fileSuffix string Suggested suffix for file name, if writing data to disk.
1) Mackey A.J., Haystead T.A. and Pearson W.R. (2002)
Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences.
Mol. Cell Proteomics 1(2):139-47.
PubMed: 12096132
DOI: 10.1074/mcp.M100004-MCP200
 
services/sss/fastm_soap.txt · Last modified: 2013/04/30 10:39 by hpm
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