# 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
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:

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.

## 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 mview script (that you just edited) is on your PATH and rehash or login again.

## 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.