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 markup, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated values).

Full documentation can be found in the on-line manual, a copy of which is also included 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 latest release of the software on GitHub can be downloaded by clicking on the ‘releases’ tab then selecting a version and archive format (zip or tar.gz).

A snapshot of the (possibly unstable) development code can be downloaded using the ‘Download ZIP’ button on the main page.

Tarballs and bzip2 archives of releases can also be found at the older SourceForge archive.

Install

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

    tar xvzf mview-1.61.tar.gz
    

    or:

    gunzip < mview-1.61.tar.gz | tar xvf -
    

    This would create a directory called mview-1.61 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-1.61/lib';
    

    and save the file.

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

Found a bug?

Please send an email to biomview _at_ 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 email 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]

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. Many other people have suggested new features and reported bugs; I hope I have acknowledged them in the change log and apologise if I have missed anyone out.