Introduction

MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats.

Inputs:

• Sequence database search: BLAST, FASTA suites.
• Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF.

Outputs:

• HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated).

The tool is used in molecular biology and biomedical research for data analyses and as a component in various bioinformatics web services. Research papers citing MView are indexed on Google Scholar.

Manual

Full documentation can be found in the manual, a copy of which is bundled with the code.

Requirements

MView is implemented in Perl, version 5 as a self-contained command line program that should run cross-platform.

Perl is generally installed on Linux, OS X, and other UNIX. MView is known to work on Windows with Strawberry Perl.

Download

• The current release can be downloaded from SourceForge as a gzip or bzip2 compressed tar archive.
• Older releases and historical download statistics can also be found on SourceForge.
• The latest code can be downloaded direct from GitHub by clicking the green "Clone or download" button and following the instructions to either clone the git repository or download a ZIP archive.

Installation

There are several ways to install MView, with further details given below.

Each method can be used by an ordinary user installing into their own account, or by a system administrator installing onto a computer with multiple users. It is assumed that Perl is already installed and on your PATH.

• Installer script

  The installer program should work on all systems, but is new and relatively experimental.

  You unpack the archive into a destination folder and run the installer from there, following the instructions. You may have to edit PATH afterwards.

  Explanation: the installer puts a small mview driver program into a folder on PATH so that it can be run easily by the user. The driver knows the location of the unpacked MView folder and starts the real MView program.

• Manual install

  This works on all systems and is the most basic, but requires that you do a little editing.

  You unpack the archive into a destination folder, edit the MView program by hand, then add the folder containing that program to PATH.

• Perl module

  This method assumes that, as well as Perl, you have some version of make installed, so may not work on all systems.

  You unpack the archive into a temporary folder and run the standard Perl module installation incantation. Unlike the other installation methods you can then delete the installation folder because all the code has been copied into Perl somewhere.

  Installing a perl Module has the advantage that there is (usually) no need to change PATH, but the disadvantage that it installs directly into your Perl installation (or personal perl folder known to Perl), which you may not want to do.

Linux, OS X, UNIX

Installer script

1. Save the archive to somewhere under your home folder then uncompress and extract it:

    tar xvzf mview-1.66.1.tar.gz
   

   This creates a sub-folder mview-1.66.1 containing all the files.

2. Change to this folder.

3. Run the command:

    perl install.pl
   

   and follow the instructions. You will be offered various places to install the driver script.

   If you know in advance the name of the folder you want to use for the driver script, you can supply it on the command line:

    perl install.pl /folder/on/my/path
   

4. If the installer couldn't find a sensible place to install the script, it chooses ~/bin and you will have to add that to your PATH, then rehash or login again.

Manual install

1. Save the archive to your software area, for example, /usr/local, then uncompress and extract it:

    tar xvzf mview-1.66.1.tar.gz
   

   This creates a sub-folder mview-1.66.1 containing all the files.

2. Change to this folder.

3. Edit the file bin/mview.

   Set a valid path for the Perl interpreter on your machine after the #! at the top of the file, for example:

    #!/usr/bin/perl
   

   Find the line:

    $MVIEW_HOME = "/path/to/mview/unpacked/folder";
   

   and change the path, in our example, to:

    $MVIEW_HOME = "/usr/local/mview-1.66.1";
   

   Save the file.

4. Finally, make sure that the bin folder containing the mview script (that you just edited) is on the user PATH, and rehash or login again.

   In our example, you would add /usr/local/mview-1.66.1/bin to the existing value of PATH, or replace any older MView path.

Windows

Installer script

1. Save the archive to somewhere under your home folder then uncompress and extract it (using an archiver like WinZip or 7-Zip, as here):

    7z x mview-1.66.1.tar.bz2
    7z x mview-1.66.1.tar
   

   This creates a sub-folder mview-1.66.1 containing all the files.

2. Change to this folder.

3. Run the command:

    perl install.pl
   

   and follow the instructions. You will be offered various places to install the driver script.

   If you know in advance the name of the folder you want to use for the driver script, you can supply it on the command line:

    perl install.pl \folder\on\my\path
   

4. If the installer couldn't find a sensible place to install the driver, it chooses C:\bin and you will have to add that to your PATH, then start a new command prompt.

Manual install

1. Save the archive to your software area, for example, C:\Program Files, then uncompress and extract it (using an archiver like WinZip or 7-Zip, as here):

    7z x mview-1.66.1.tar.bz2
    7z x mview-1.66.1.tar
   

   This creates a sub-folder mview-1.66.1 containing all the files.

2. Change to this folder.

3. Edit the file bin\mview.

   Find the line:

    $MVIEW_HOME = "/path/to/mview/unpacked/folder";
   

   and change the path, in our example, to:

    $MVIEW_HOME = "C:\Program Files\mview-1.66.1";
   

   Save the file.

4. Finally, make sure that the bin folder containing the mview script (that you just edited) is on the user PATH, then start a new command prompt.

   In our example, you would append C:\Program Files\mview-1.66.1\bin to the existing value of PATH, or replace any older MView path.

Perl module

1. Save the archive then uncompress and extract it (Linux, OS X, UNIX):

    tar xvzf mview-1.66.1.tar.gz
   

   or (Windows, using an archiver WinZip, 7-Zip, etc.)

    7z x mview-1.66.1.tar.bz2
    7z x mview-1.66.1.tar
   

   This creates a sub-folder called mview-1.66.1 containing all the files.

2. Change to this folder.

You can now use one of the following sets of instructions to do the install:

3. Run:

    perl Makefile.PL
    make install
   

   which attempts to install into the Perl distribution.

4. Or run:

    perl Makefile.PL INSTALL_BASE=/usr/local
    make install
   

   which attempts to install under the given folder. In this UNIX example you need write access to /usr/local and users will need /usr/local/bin on their PATH.

5. Or, if you have a local::lib setup, you can install mview there:

    perl Makefile.PL $PERL_MM_OPT
    make install
   

6. Finally, the unpacked archive can be deleted since the important components have been copied elsewhere.

Testing

Each release of MView is regression tested against hundreds of sample data inputs for all the sequence database search and alignment formats and versions thereof that are supported, together with known edge cases. This is well over 0.5GB of material, so it's not currently available externally.

Found a bug?

Please open an issue on the MView issue tracker or send an email to [email protected].

If MView isn't able to parse your input file or produces a warning message, it would be very helpful if you can include/attach the data file in your message so that I can (1) quickly reproduce the error, and (2) add the example to the test suite.

Citation

If you use MView in your work, please cite:

Brown, N.P., Leroy C., Sander C. (1998). MView: A Web compatible database search or multiple alignment viewer. Bioinformatics. 14 (4):380-381. [PubMed]

Copyright and licence

MView is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Acknowledgements

People who contributed early code or suggestions include C. Leroy and other members of the former Sander group at EBI. Useful suggestions relating to the EBI sequence database search services have come from R. Lopez, W. Li and H. McWilliam at EBI. Thanks to the many other people who have suggested new features and reported bugs. Finally, thank you to everyone who has cited MView in their publications.