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EBIEMBL-EBI Web Servicesservicessssfasta_soap
Table of Contents

FASTA (SOAP)

Description

FASTA 1) (pronounced FAST-Aye) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison. This program achieves a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised searches for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word hits to identify potential matches before attempting the more time consuming optimised search. The trade-off between speed and sensitivity is controlled by the ktup parameter, which specifies the size of the word. Increasing the ktup decreases the number of background hits. Not every word hit is investigated but instead initially looks for segment's containing several nearby hits.

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: FastaCliClient.exe; Source: AbstractWsClient.cs, FastaClient.cs, FastaCliClient.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: Fasta_Axis1.jar; Source: AbstractWsToolClient.java, FastaClient.java Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in lib-1.4.zip.
Perl fasta_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 FASTA SOAP service: http://www.ebi.ac.uk/Tools/services/soap/fasta?wsdl

The Kissinger Research Group, University of Georgia provide a SAWSDL for the FASTA (SOAP) web service, which is annotated using OBIws: http://mango.ctegd.uga.edu/jkissingLab/SWS/Wsannotation/resources/fasta.sawsdl

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. Required.
stype string Query sequence type. One of: dna, rna or protein. Required.
matrix string Scoring matrix to be used in for protein search.
match_scores string Match/missmatch scores for nucleotide search.
gapopen int Score for the initiation of a gap.
gapext int Score for each base/residue in a gap.
hsps boolean Enable/disable output of multiple alignments per-hit.
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.
annotsym string Annotation symbols to appear on alignments for query and/or database.
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 sequence. The use of fasta formatted sequence is recommended. 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.

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 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 for 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) Pearson W.R. and Lipman D.J. (1988)
Improved tools for biological sequence comparison.
Proc. Natl. Acad. Sci. U.S.A. 85(8):2444-8
PubMed: 3162770
DOI: 10.1073/pnas.85.8.2444
 
services/sss/fasta_soap.txt · Last modified: 2013/04/30 10:39 by hpm
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