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.

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.

Install

Linux, Apple, UNIX

There are different approaches depending on whether you are installing for your own use or as a site administrator for multiple users.

Personal use

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 called `mview-1.66.1' containing all the files.

2. Change to this folder.

3. Run the command:

    perl install.pl
   

   and follow the instructions. The installer creates a driver script pointing to wherever you just unpacked MView. It offers you various places to install this driver so that it is on your `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.

Site administrator for multiple users

You can use the `install.pl' script as above, or install manually:

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 called `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.

As a Perl package

MView can be installed as a Perl package:

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 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 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 crucial components have been installed elsewhere.

Windows

MView requires a Perl installation and is known to work with Strawberry Perl for Windows.

There are different approaches depending on whether you are installing for your own use or as a site administrator for multiple users.

Personal use

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.gz
    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.

3. Run the command:

    perl install.pl
   

   and follow the instructions. The installer creates a driver script pointing to wherever you just unpacked MView. It offers you various places to install this driver so that it is on your `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.

Site administrator for multiple users

You can use the `install.pl' script as above, or install manually:

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

    7z x mview-1.66.1.tar.gz
    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.

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:\Programs\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:\Programs\mview-1.66.1\bin' to the existing value of PATH', or replace any older MView path.

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.