EMBOSS Matcher (Protein Alignment)

Introduction

EMBOSS Matcher identifies local similarities in two input sequences using a rigorous algorithm based on Bill Pearson's lalign application, version 2.0u4 (Feb. 1996)

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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 be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot format. Partially formatted sequences are not accepted. 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, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot) can be used as input for the sequence similarity search. 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 be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot format. Partially formatted sequences are not accepted. 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, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot) can be used as input for the sequence similarity search. 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 Name Abbreviation
BLOSUM30 EBLOSUM30
BLOSUM35 EBLOSUM35
BLOSUM40 EBLOSUM40
BLOSUM45 EBLOSUM45
BLOSUM50 EBLOSUM50
BLOSUM55 EBLOSUM55
BLOSUM60 EBLOSUM60
BLOSUM62 EBLOSUM62
BLOSUM65 EBLOSUM65
BLOSUM70 EBLOSUM70
BLOSUM75 EBLOSUM75
BLOSUM80 EBLOSUM80
BLOSUM85 EBLOSUM85
BLOSUM90 EBLOSUM90
BLOSUM Clustered EBLOSUMN
PAM 10 EPAM10
PAM 20 EPAM20
PAM 30 EPAM30
PAM 40 EPAM40
PAM 50 EPAM50
PAM 60 EPAM60
PAM 70 EPAM70
PAM 80 EPAM80
PAM 90 EPAM90
PAM 100 EPAM100
PAM 110 EPAM110
PAM 120 EPAM120
PAM 130 EPAM130
PAM 140 EPAM140
PAM 150 EPAM150
PAM 160 EPAM160
PAM 170 EPAM170
PAM 180 EPAM180
PAM 190 EPAM190
PAM 200 EPAM200
PAM 210 EPAM210
PAM 220 EPAM220
PAM 230 EPAM230
PAM 240 EPAM240
PAM 250 EPAM250
PAM 260 EPAM260
PAM 270 EPAM270
PAM 280 EPAM280
PAM 290 EPAM290
PAM 300 EPAM300
PAM 310 EPAM310
PAM 320 EPAM320
PAM 330 EPAM330
PAM 340 EPAM340
PAM 350 EPAM350
PAM 360 EPAM360
PAM 370 EPAM370
PAM 380 EPAM380
PAM 390 EPAM390
PAM 400 EPAM400
PAM 410 EPAM410
PAM 420 EPAM420
PAM 430 EPAM430
PAM 440 EPAM440
PAM 450 EPAM450
PAM 460 EPAM460
PAM 470 EPAM470
PAM 480 EPAM480
PAM 490 EPAM490
PAM 500 EPAM500

Default value is: BLOSUM62 [EBLOSUM62]

Additional information

Gap Open Penalty

Pairwise alignment score for the first residue in a gap.

Default value is: 14

Additional information

Gap Extend Penalty

Pairwise alignment score for each additional residue in a gap.

Default value is: 4

Additional information

Alternative matches

Show additional alignments

Default value is: 1

Output formats

Pairwise sequences format

Value Description
pair The sequences have the markup line between them
markx0 This is the standard default output format used by Bill Pearson's suite of FASTA programs
markx1 This 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'
markx2 This 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
markx3 This 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
markx10 This 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
srspair This is very similar in style to pair format
score This does not display the sequence alignment. It shows only the names of the sequences, the length of the alignment and the score

Default value is: pair

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 Jun) Trends in genetics : TIG 16 (6) :276-7
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600