MView

Introduction

MView reformats the results of a sequence database search (BLAST, FASTA, etc) or a multiple alignment (MSF, PIR, CLUSTAL, etc) adding optional HTML mark-up to control colouring and web page layout. MView is not a multiple alignment program, nor is it a general purpose alignment editor.

Official Website
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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 Alignment

Input Window

Sequence similarity search result (e.g. BLAST or FASTA search report) or a multiple sequence alignment.

File Upload

A file containing a sequence similarity search result (e.g. BLAST or FASTA search report) or a multiple sequence alignment.

Alignment sequences type

Indicates if the sequences to align are protein or nucleotide (DNA/RNA).

Type Value
Protein protein
DNA dna

Default value is: Protein [protein]

Step 2 - Set Input Parameters

Input Format

Format of the input sequence similarity search result or multiple sequence alignment to be processed.

Format Description Value
AUTOMATIC AUTOMATIC mode automatic
BLAST BLAST search report format blast
FASTA FASTA search report format fasta
PEARSON Pearson/fasta sequence format pearson
CLUSTAL CLUSTAL alignment format clustal
MSF MSF alignment format msf
PIR PIR sequence format pir
HSSP HSSP format hssp

Default value is: AUTOMATIC [automatic]

Step 3 - Set Output Parameters

Output Format

Output format for the alignment.

Format Description Value
NEW MView alignment format new
PEARSON Pearson/fasta sequence format pearson
MSF MSF alignment format msf
PIR PIR sequence format pir
RDB RDB format rdb
PLAIN Plain format plain

Default value is: NEW [new]

HTML Markup

Amount of HTML markup to be used in the result.

Markup Value
DATA data
OFF off

Default value is: DATA [data]

CSS

Use Cascading Style Sheets

Option Value
ON true
OFF false

Default value is: ON [true]

PCID

Compute percent identities with respect to

PCID Value
aligned aligned
hit hit
reference reference

Default value is: aligned

ALIGNMENT

Show or hide the aligned sequences.

Option Value
ON true
OFF false

Default value is: ON [true]

RULER

Show or hide the ruler showing the sequence coordinates.

Option Value
ON true
OFF false

Default value is: ON [true]

OUTPUT ALIGNMENT WIDTH

Width of output alignment.

Value
50
60
80
100
120

Default value is: 80

Coloring

Basic style of coloring

Coloring Value
Identity identity
Any any
Consensus consensus
Group group
N/A none

Default value is: Identity [identity]

Color Map

Color map

Map Description Value
N/A No color map none
CCLUSTAL Protein consensus: highlight equivalence class CCLUSTAL
CLUSTAL Protein: highlight amino acid physicochemical properties CLUSTAL
CHARGE Protein: highlight charged amino acids CHARGE
CYS Protein: highlight cysteines CYS
D1 DNA: highlight purine versus pyrimidine D1
D2 DNA: highlight match versus mismatch under consensus coloring schemes D2
DC1 DNA consensus: highlight ring type DC1
GPCR Protein: GPCRdb color scheme for Gert Vriend GPCR
HXLIN Kuang Lin's colour neural net derived scheme HXLIN
NARDI Protein: highlight amino acid physicochemical properties NARDI
P1 Protein: highlight amino acid physicochemical properties P1
PC1 Protein consensus: highlight equivalence class PC1
POLAR1 Protein: highlight charged and polar amino acids POLAR1
RED Red RED

Default value is: N/A [none]

Group Map

Group map

Map Description Value
N/A None none
CYS Protein consensus: report conserved cysteines only CYS
D1 DNA consensus: report conserved ring types D1
P1 Protein consensus: report conserved physicochemical classes P1

Default value is: N/A [none]

Show Consensus

Show or hide consensus sequence derived from the alignment.

Label Description Value
ON true
OFF false

Default value is: ON [true]

Consensus Concoloring

Basic style of consensus coloring

Coloring Value
Any any
Identity identity
N/A none

Default value is: Any [any]

Consensus Color Map

Consensus color map

Map Description Value
N/A No color map none
CCLUSTAL Protein consensus: highlight equivalence class CCLUSTAL
CLUSTAL Protein: highlight amino acid physicochemical properties CLUSTAL
CHARGE Protein: highlight charged amino acids CHARGE
CYS Protein: highlight cysteines CYS
D1 DNA: highlight purine versus pyrimidine D1
D2 DNA: highlight match versus mismatch under consensus coloring schemes D2
DC1 DNA consensus: highlight ring type DC1
GPCR Protein: GPCRdb color scheme for Gert Vriend GPCR
HXLIN Kuang Lin's colour neural net derived scheme HXLIN
NARDI Protein: highlight amino acid physicochemical properties NARDI
P1 Protein: highlight amino acid physicochemical properties P1
PC1 Protein consensus: highlight equivalence class PC1
POLAR1 Protein: highlight charged and polar amino acids POLAR1
RED Red RED

Default value is: N/A [none]

Consensus Group Map

Consensus group map

Map Description Value
N/A None none
CYS Protein consensus: report conserved cysteines only CYS
D1 DNA consensus: report conserved ring types D1
P1 Protein consensus: report conserved physicochemical classes P1

Default value is: N/A [none]

CONGAPS

Count gaps during consensus compuatations

Option Value
ON true
OFF false

Default value is: ON [true]

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

MView: a web-compatible database search or multiple alignment viewer.
(1998) Bioinformatics (Oxford, England) 14 (4) :380-1
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