Page tree
Skip to end of metadata
Go to start of metadata

Input form  |  Web services  |  Help & Documentation  |  Bioinformatics Tools FAQ

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

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.

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]

Additional information Read more about matrices

Gap Open Penalty

Pairwise alignment score for the first residue in a gap.

Default value is: 10

Additional information Read more about gap penalties

Gap Extend Penalty

Pairwise alignment score for each additional residue in a gap.

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

Default value is: false

End Gap Open Penalty

Score taken away when an end gap is created.

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.

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).

References

EMBOSS: the European Molecular Biology Open Software Suite.
(2000 June 01) Trends in genetics : TIG 16 (6) :276-277
PMID: 10827456 The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 April 06) Nucleic acids research 43 (W1) :W580-4
PMID: 25845596 Analysis Tool Web Services from the EMBL-EBI.
(2013 May 13) Nucleic acids research 41 (Web Server issue) :W597-600
PMID: 23671338

  • No labels