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

Instructions for a Linux or other UNIX-like system (Apple, BSD, etc.) follow. The procedure is similar for Windows.

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

    tar xvzf mview-1.64.tar.gz
   

   or

    gunzip < mview-1.64.tar.gz | tar xvf -
   

   This would create a directory called mview-1.64 and place all the files under there.

2. Change to this directory and load bin/mview into an editor.

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

    #!/usr/bin/perl
   

4. Find the use lib '/path/to/mview/lib'; line and change it, in our example, to:

    use lib '/usr/local/mview-1.64/lib';
   

   and save the file.

5. Finally, make sure that the directory containing the mview script (that you just edited) is on your PATH and rehash or login again.

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 biomview@gmail.com.

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.