MView¶

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.

                                1 [        .         .         .         .         :         .         .         ] 80
1 sp|P00533.2|EGFR_HUMAN  100.0%  FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 sp|Q9I7F7.3|PR2_DROME    35.7%  ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 sp|Q08881.1|ITK_HUMAN    32.9%  LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 sp|Q13308.2|PTK7_HUMAN   21.2%  IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 sp|P34265.4|KIN31_CAEEL  31.5%  VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
  consensus/90%                   .......G.G.FG.V........................VA.K.................E...M...............
  consensus/80%                   ....K..G.G.FG.V..G.....................VA.K.................EA..M....H...V.L.G..

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.

Documentation¶

Short contents:

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 and UNIX systems. 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:

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 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]

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.