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Introduction

EMBOSS Needle reads two input sequences and writes their optimal global sequence alignment to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length.

Official Website

Download Software

Important Note

  • 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 EMBOSS Needle

EMBOSS Needle can be accessed via

Web Form

Web interface for EMBOSS Needle is available at : https://www.ebi.ac.uk/Tools/psa/emboss_needle (protein) https://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html (nucleotide)

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

A free text (raw) list of sequences is simply a block of characters representing several DNA/RNA or Protein sequences. A sequence can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. 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.

First Sequence File Upload

A file containing valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) can be used as input for the sequence similarity search. (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

A free text (raw) list of sequences is simply a block of characters representing several DNA/RNA or Protein sequences. A sequence can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. 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.

Second Sequence File Upload

A file containing valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) can be used as input for the sequence similarity search. (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.

Step 2 - Set alignment options

Matrix

Default substitution scoring matrices.


 Protein
Matrix NameAbbreviation
BLOSUM30EBLOSUM30
BLOSUM35EBLOSUM35
BLOSUM40EBLOSUM40
BLOSUM45EBLOSUM45
BLOSUM50EBLOSUM50
BLOSUM55EBLOSUM55
BLOSUM60EBLOSUM60
BLOSUM62EBLOSUM62
BLOSUM65EBLOSUM65
BLOSUM70EBLOSUM70
BLOSUM75EBLOSUM75
BLOSUM80EBLOSUM80
BLOSUM85EBLOSUM85
BLOSUM90EBLOSUM90
BLOSUM ClusteredEBLOSUMN
PAM 10EPAM10
PAM 20EPAM20
PAM 30EPAM30
PAM 40EPAM40
PAM 50EPAM50
PAM 60EPAM60
PAM 70EPAM70
PAM 80EPAM80
PAM 90EPAM90
PAM 100EPAM100
PAM 110EPAM110
PAM 120EPAM120
PAM 130EPAM130
PAM 140EPAM140
PAM 150EPAM150
PAM 160EPAM160
PAM 170EPAM170
PAM 180EPAM180
PAM 190EPAM190
PAM 200EPAM200
PAM 210EPAM210
PAM 220EPAM220
PAM 230EPAM230
PAM 240EPAM240
PAM 250EPAM250
PAM 260EPAM260
PAM 270EPAM270
PAM 280EPAM280
PAM 290EPAM290
PAM 300EPAM300
PAM 310EPAM310
PAM 320EPAM320
PAM 330EPAM330
PAM 340EPAM340
PAM 350EPAM350
PAM 360EPAM360
PAM 370EPAM370
PAM 380EPAM380
PAM 390EPAM390
PAM 400EPAM400
PAM 410EPAM410
PAM 420EPAM420
PAM 430EPAM430
PAM 440EPAM440
PAM 450EPAM450
PAM 460EPAM460
PAM 470EPAM470
PAM 480EPAM480
PAM 490EPAM490
PAM 500EPAM500

Default value is: BLOSUM62 [EBLOSUM62]

 Nucleotide
Matrix NameAbbreviation
DNAfullEDNAFULL
DNAmatEDNAMAT

Default value is: DNAfull [EDNAFULL]


Additional information Read more about matrices

Gap Open Penalty

Pairwise alignment score for the first residue in a gap.

Values : 100, 50, 25, 20,15,10, 5, 1

Default value is: 10

Additional information Read more about gap penalties

Gap Extend Penalty

Pairwise alignment score for each additional residue in a gap.


 List Values

0.0005 
0.001 
0.05 
0.1 
0.2 
0.4 
0.6 
0.8 
1.0 
5.0 
10.0

Default value is: 0.5

Additional information Read more about gap penalties

Output formats

Pairwise sequences format (example output formats).

ValueDescription
pairThe sequences have the markup line between them
markx0This is the standard default output format used by Bill Pearson's suite of FASTA programs
markx1This is an alternative output format used by Bill Pearson's suite of FASTA programs in which identities are not marked. Instead conservative replacements are denoted by 'x' and non-conservative substitutions by 'X'
markx2This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the residues in the second sequence are only shown if they are different from the first
markx3This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the aligned sequences are displayed in FASTA sequence format. These can be used to build a primitive multiple alignment
markx10This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the aligned sequences are displayed in FASTA sequence format and the sequence length, alignment start and stop information is given in lines starting with a ';' character just after the title line for each sequence. It is intended to be easily parsed by other programs
srspairThis is very similar in style to pair format
scoreThis does not display the sequence alignment. It shows only the names of the sequences, the length of the alignment and the score
clustalClustal alignment format without base/residue numbering
fastaPearson or FASTA sequence format
msfMultiple Sequence File (MSF) alignment format
nexusNEXUS alignment format
phylipPHYLIP interleaved alignment format
selexSELEX alignment format

Default value is: pair

End Gap Penalty

Apply end gap penalty

Values: true / false

Default value is: false

End Gap Open Penalty

Score taken away when an end gap is created.

Values: 100, 50, 25, 20, 15, 10, 5, 1

Default value is: 10

End Gap Extend Penalty

Penalty is added to the end gap penalty for each base or residue in the end gap. This is how long end gaps are penalized.


 List Values

0.0005
0.001
0.05
0.1
0.2
0.4
0.6
0.8
1.0
5.0
10.0


Default value is: 0.5

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
Perlemboss_needle.plLWP and XML::Simple

Python

emboss_needle.py

xmltramp2

For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.

WADL

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


 List Tool Parameters

Parameters

Command line parameter

--matrix
GAP OPEN--gapopen
GAP EXTEND--gapext
OUTPUT FORMAT--format
END GAP PENALTY--endweight
END GAP OPEN--endopen
END GAP EXTEND--endextend

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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 EMBOSS needle (SOAP) service: http://www.ebi.ac.uk/Tools/services/soap/emboss_needle?wsdl


 List Methods
MethodsDescriptionArgumentsReturns

getParameters()

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

DgetParameterDetails(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 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
matrixstringScoring matrix.
gapopenrealGap creation penalty.
gapextendrealGap extension penalty.
endweightbooleanEnable/disable penalties for end gaps.
endopenrealGap creation penalty for end gap.
endextrealGap extension penalty for end gap.
formatstringOutput alignment format.
stypestringSequence type.
asequencestringFirst sequence.
bsequencestringSecond 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
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

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


 List Endpoints

Endpoints

DescriptionArgumentsReturns

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/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/emboss_needle/parameterdetails/matrix

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/parameterdetails/gapopen

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/parameterdetails/gapext

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/parameterdetails/endweight

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/parameterdetails/endopen

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/parameterdetails/endextend

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/parameterdetails/format

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/parameterdetails/stype

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

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/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/emboss_needle/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/emboss_needle/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/emboss_needle/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/emboss_needle/result/<jobid>/out

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

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

https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/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 

EMBOSS

EMBOSS Needle

EBI  Web Services

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