pfamscan 的使用_PfamScan Help and Documentation

Introduction

PfamScan is used to search a FASTA sequence against a library of Pfam HMM.

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Important Note

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.

How to Access PfamScan

PfamScan can be accessed via

Web Form

Web interface for PfamScan is available at : https://www.ebi.ac.uk/Tools/pfa/pfamscan/

How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:The first steps are usually where the user sets the tool input (e.g. sequences, databases...)

In the following steps, the user has the possibility to change the default tool parameters

And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Input Sequences

Input Sequence

The input sequence can be entered directly into this form. The sequence can be in FASTA or UniProtKB/Swiss-Prot format. A partially formatted sequence is not accepted. (See example input formats). Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.

Sequence File Upload

A file containing a valid sequence in FASTA or UniProtKB/Swiss-Prot format can be used as input. (See example input formats). Word processor files may yield unpredictable results as hidden/control characters may be present. It is best to save files with the Unix format option to avoid hidden Windows characters.

Step 2 - Set options

Database

The database(s) to search.

NameValuePfam-Apfam-a

Default value is: Pfam-A [pfam-a]

Expectation Value

Expectation value cut-off.

List Values

1e-3001e-1001e-501e-101e-50.00010.0010.1125102050

Default value is: 10

Active Site Prediction

Predict active site residues for Pfam-A matches.

NameValueyestrue

nofalse

Default value is: no [false]

Output Format

NameValueDescriptionJSONjsonJSON output format.

Plain TexttxtPlain text output format.

Default value is: JSON [json]

Step 3 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).

Web Services

Web Services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines.

For an introduction on how to run these clients and use them in workflows please see the webinar series.

REST API

The Representational State Transfer (REST) 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.

WADL

List Tool Parameters

ParametersCommand line parameterDescriptionDATABASE--databaseThe database(s) to search

EXPECTATION VALUE--evalueExpectation value cut-off

ACTIVE SITE PREDICTION--aspPredict active site residues for Pfam-A matches

OUTPUT FORMAT--formatOutput format

SOAP API

The Simple Object Access Protocol (SOAP) sample clients are provided for a number of programming languages. For details of how to use these clients, downloadthe client and run the program without any arguments.

WSDL

List Methods

MethodsDescriptionArgumentsReturns

getParameters()Get a list of the parameter names.nonea list of strings giving the names of the parameters.

getParameterDetails(parameterId)Get details of a specific parameter.parameterId: identifier/name of the parameter to fetch details of.a wsParameterDetails describing the parameter and its values.

run(email, title, params)Submit a job to the service.email: (required) user e-mail address. See Why do you need my e-mail address?

title: job title. Default: ””.

params: (required) parameters for the tool. These are described by the InputParameters data structure.a string containing the job identifier (jobId).

getStatus(jobId)Get the status of a submitted job.jobId: (required) job identifier.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.

getResultTypes(jobId)Get the available result types for a finished job.jobId: (required) job identifier.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.jobId: (required) job identifier.

type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.

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.

List Datatypes

InputParameters

The input parameters for the job:

AttributeTypeDescription

databasestringDatabase to search.

evaluedoubleExpectation value (E-value) threshold.

aspbooleanActive Site Prediction.

formatstringOutput format.

sequencestringQuery protein sequence. The use of fasta formatted sequence is recommended.

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).

AttributeTypeDescription

namestringName of the parameter.

descriptionstringDescription of the parameter, suitable for use in option help interfaces.

typestringData type of the parameter.

valueslist of wsParameterValueList of valid values for the option.

wsParameterValue

Description of a tool parameter value. Used in wsParameterDetails.

AttributeTypeDescription

labelstringDisplay name of the value, for use in interfaces.

valuestringString representation of the value to be passed to the tool parameter.

defaultValuebooleanFlag indicating if this value is the default.

propertieslist of wsPropertyList of key/value pairs providing further information.

wsProperty

Properties of a tool parameter value. Used in wsParameterValue.

AttributeTypeDescription

keystringProperty name

valuestringProperty value

wsRawOutputParameter

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

AttributeTypeDescription

namestringParameter name

valuelist of stringParameter value

wsResultType

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

AttributeTypeDescription

identifierstringIdentifier for the result type. Passed as type to getResult(jobId, type, parameters).

labelstringDisplay name for use in user interfaces.

descriptionstringDescription of the result type, for use in help interfaces.

mediaTypestringMIME type of the returned data.

fileSuffixstringSuggested suffix for file name, if writing data to disk.

Open API Interface

List Endpoints

EndpointsDescriptionArgumentsReturns

Get a list of the parameter names.noneA list of strings giving the names of the parameters.

https://www.ebi.ac.uk/Tools/services/rest/pfamscan/runSubmit a job to the service.email: (required) user e-mail address. See Why do you need my e-mail address?

title: job title. Default: ””.

params: (required) parameters for the tool. These are described by the InputParameters data structure.A string containing the job identifier (jobId).

https://www.ebi.ac.uk/Tools/services/rest/pfamscan/status/Get the status of a submitted job.jobId: (required) job identifier.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.

https://www.ebi.ac.uk/Tools/services/rest/pfamscan/resulttypes/Get the available result types for a finished job.jobId: (required) job identifier.Returns: a list of wsResultType data structures describing the available result types.

https://www.ebi.ac.uk/Tools/services/rest/pfamscan/result//out

https://www.ebi.ac.uk/Tools/services/rest/pfamscan/result//sequenceGet the result of a job of the specified type.jobId: (required) job identifier.

type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.

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.

Common Workflow Language

CWL (Common Workflow Language) implementation for consumingEMBL-EBI Bioinformatics Web Services tools' clients

For details, see CWL Workflows page.

Reference