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Introduction

The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

Official Website

Download Software

Important Note

  • There is a limit of 1MB
  • PSA tool algorithms are NOT intended to produce genome synteny maps.
  • 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 GeneWise

GeneWise can be accessed via

Web Form

Web interface for GeneWise is available at : https://www.ebi.ac.uk/Tools/psa/genewise/

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

First Input Sequence

The protein sequence can be entered directly into this form. The sequence can be in GCG, FASTA, GenBank, PIR, NBRF, PHYLIP 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. 

A file containing a valid protein sequence in any format (GCG, FASTA, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot) can be used as input for the sequence comparison. (See example input formats). Word processors files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters. 

Second Input Sequence

The DNA sequence to be compared can be entered directly into the form. The sequence must be in a recognised format eg. GCG, FASTA, EMBL or GenBank. Partially formatted sequences are 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. There is a limit of 1MB for the sequence entry.

Second Sequence File Upload

A file containing valid a DNA sequence in any format (GCG, FASTA, EMBL or GenBank) can be used as input for the comparison. (See example input formats). Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters. There is a limit of 1MB for the sequence entry.

Step 2 - Set alignment options

Show Parameters

Show parameters in the output alignmment, as in genewise.

Values: ON / OFF

Default value is: ON [true]

Pretty ASCII

Show pretty ASCII alignment viewing, as in genewise.

Values: ON / OFF

Default value is: ON [true]

Gene Structure

Show gene structure, as in genewise

Values: ON / OFF

Default value is: ON [true]

Protein Translation

Show protein translation, breaking at frameshifts.

Values: ON / OFF

Default value is: ON [true]

cDNA

Show cDNA, as in genewise.

Values: ON / OFF

Default value is: ON [true]

EMBL Feature Table

EMBL feature table format with CDS key.

Values: ON / OFF

Default value is: ON [true]

Ace File Gene Structure

Show Ace file gene structure, as in genewise.

Values: ON / OFF

Default value is: ON [true]

GFF Output

Show Gene Feature Format file, as in genewise.

Values: ON / OFF

Default value is: ON [true]

(example output format)

EMBL Feature For diana

Show EMBL FT format suitable for diana.

Values: ON / OFF

Default value is: ON [true]

Local/Global Mode

Model in local/global mode. You should only put the model in global mode if you expect your protein homolog to have homology from start to end to the gene in the DNA sequence.

LabelAbbreviation
Locallocal
Globalglobal

Default value is: Local [local]

Splice Site

Using splice model or GT/AG? Use the full blown model for splice sites, or a simplistic GT/AG. Generally if you are using a DNA sequence which is from human or worm, then leave this on. If you are using a very different (eg plant) species, switch it off.

LabelAbbreviation
Modelledmodel
GT/AG onlyflat

Default value is: GT/AG only [flat]

Random (Null) Model

The probability of the model has to compared to an alternative model (in fact to all alternative models which are possible) to allow proper Bayesian inference. This causes considerable difficulty in these algorithms because from a algorithmical point of view we would probably like to use an alternative model which is a single state, like the random model in profile-HMMs, where we can simply 'log-odd' the scored model, whereas from a biological point of view we probably want to use a full gene predicting alternative model. In addition we need to account for the fact that the protein HMM or protein homolog probably does not extend over all the gene sequence, nor in fact does the gene have to be the only gene in the DNA sequence. This means that there are very good splice sites/poly-pyrimidine tracts outside of the 'matched' alignment can severely de-rail the alignment.

LabelAbbreviation
Synchronous modelsyn
Flat modelflat

Default value is: Synchronous model [syn]

Algorithm

The solutions is different in the genewise21:93 compared to the genewise 6:23 algorithms. (1) In 6:23 we force the external match portions of the homology model to be identical to the alternative model, thus cancelling each other out. This is a pretty gross approximation and is sort of equivalent to the intron tie'ing. It makes things algorithmically easier... However this means a) 6:23 is nowhere near a probabilistic model and b) you really have to used a tied intron model in 6:23 otherwise very bad edge effects (final introns being ridiculously long) occur. (2) In 21:93 we have a full probabilistic model on each side of the homology segment. This is not reported in the -pretty output but you can see it in the -alb output if you like. Do not trust the gene model outside of the homology segment however. By having these external gene model parts we can use all the gene model features safe in the knowledge that if the homology segments do not justify the match then the external part of the model will soak up the additional intron/py-tract/splice site biases.

LabelAbbreviation
GeneWise 623623
GeneWise 21932193

Default value is: GeneWise 623 [623]

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).

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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.

LanguageDownloadRequirements
Perlgenewise.plLWP and XML::Simple

Python

genewise.py

xmltramp2

For an introduction on how to run these clients and use them in workflows please see the 'EMBL-EBI, programmatically: take a REST from manual searches' webinar series.

WADL

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

Tool Parameters

Parameters

Command line parameter

SHOW PARAMETERS

--para
PRETTY ASCII--pretty
GENE STRUCTURE--genes
TRANSLATION--trans
cDNA--cdna
EMBL FEATURE--embl
ACE FILE GENE STRUCTURE--ace
GFF OUTPUT--gff
EMBL feature for Diana--diana
LOCAL / GLOBAL MODE--init
SPLICE SITE--splice
RANDOM (NULL) MODEL--random
ALOGORITHM--alg

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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, download the client and run the program without any arguments.

WSDL

The WSDL for the GeneWise (SOAP) service: http://www.ebi.ac.uk/Tools/services/soap/genewise?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.

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
parabooleanEnable/disable display of parameters in output.
prettybooleanEnable/disable pretty ASCII alignment output.
genesbooleanEnable/disable gene structure display.
transbooleanEnable/disable protein translation display.
cdnabooleanEnable/disable cDNA display.
emblbooleanEnable/disable EMBL-Bank feature table format output.
acebooleanEnable/disable Ace file gene structure output.
gffbooleanEnable/disable Gene Feature Format (GFF) output.
dianabooleanEnable/disable EMBL-Bank feature table format suitable for diana.
initstringModel in local/global mode.
splicestringUsing splice model or GT/AG?.
randomstringRandom (Null) Model.
algstringAlgorithm.
asequencestringProtein sequence.
bsequencestringDNA sequence.

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
keystring
valuestring

wsRawOutputParameter

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

AttributeTypeDescription
namestring
valuelist of string

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.

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Open API Interface

https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=genewise


 List Endpoints

Endpoints

DescriptionArgumentsReturns

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameters

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/genewise/parameterdetails/para

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/pretty

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/genes

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/trans

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/cdna

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/embl

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/ace

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/gff

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/diana

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/init

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/splice

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/random

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/alg

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/asequence

https://www.ebi.ac.uk/Tools/services/rest/genewise/parameterdetails/bsequence

Get details of a specific parameter.parameterdetail: identifier/name of the parameter to fetch details of.A wsParameterDetails describing the parameter and its values.

https://www.ebi.ac.uk/Tools/services/rest/genewise/run

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).

https://www.ebi.ac.uk/Tools/services/rest/genewise/status/<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.

Further details can be found in Synchronous and Asynchronous Access: Job Dispatcher.

https://www.ebi.ac.uk/Tools/services/rest/genewise/resulttypes/<jobid>

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/genewise/result/<jobid>/out

https://www.ebi.ac.uk/Tools/services/rest/genewise/result/<jobid/error

https://www.ebi.ac.uk/Tools/services/rest/genewise/result/<jobid>/asequence

https://www.ebi.ac.uk/Tools/services/rest/genewise/result/<jobid>/bsequence

https://www.ebi.ac.uk/Tools/services/rest/genewise/result/<jobid>/aln

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.

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Common Workflow Language

CWL (Common Workflow Language) implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients are available at https://github.com/ebi-wp/webservice-cwl

For details, see CWL Workflows page. 

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Reference 

GeneWise

EBI  Web Services

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