MView

MView - Introduction

MView is a tool for converting the results of a sequence database search (BLAST, FASTA, etc.) into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment (MSF, PIR, CLUSTALW, etc.) can be processed. In either case, the output is simply HTML, so the result is platform independent and does not require a separate application or applet to be loaded. MView is NOT a multiple alignment program, nor is it a general purpose alignment editor.

Release 1.40 (12 February 99)

New option -css allows colouring of alignments using Cascading Style Sheets for more control and visual impact [example]. Style sheets can be exported and imported.
New options -html, -title, -pagecolor, -textcolor, -linkcolor, -alinkcolor, -vlinkcolor, -alncolor, -symcolor, -gapcolor give more control of HTML markup. Options -body, -contrast obsolete.
A new consensus alignment colouring mode -coloring group colours residues according to a consensus threshold like the older -coloring consensus mode, but uses the colour scheme of the chosen consensus group definitions rather than that of the residues themselves.
New option -dna switches on DNA/RNA alignment colouring and consensus group schemes instead of protein.

Release 1.39 (11 November 98)

New option -con_gaps mode. Consensus colouring and consensus line computations normally count gap characters, so that sections of the alignment may be uncoloured and the consensus line reduced to gaps where the non-gap count falls below the threshold. Setting -con_gaps off prevents this, allowing sequence-only based consensus thresholding.

Release 1.38 (2 November 98)

New option -hsp method allows control of the HSPs (NCBI BLAST 1.4) or gapped alignments (WU-BLAST 2.0, NCBI BLAST 2.0) used to construct alignment rows. Three processing methods are available with the : (1) 'ranked' [default] selects only the fragment(s) that are reflected in the search ranking; (2) 'all' fragments are selected for tiling; (3) 'discrete' selects all fragments, but allocates a separate alignment row for each. Per BLAST program details of this are available.

Further information

Frequently Asked Questions
Example output

System requirements

MView and its underlying class libraries are implemented in Perl, version 5, for UNIX, and should be easily portable to other systems.

As of MView release 1.40, the code requires a minimum of perl version 5.004 and has been tested with 5.004_03/04 and 5.005_02. However, if you only have perl 5.003, you can run older versions of MView, also available from the ftp site.

Formatting and colouring of HTML alignments requires a fixed-width font (eg., Courier) and support for the <FONT> tag, so a recent version of a browser such as Netscape is recommended. In particular, use of style sheets as of MView release 1.40 requires that your browser supports HTML 4.0.

Obtaining the software

The latest version of the software is available free for FTP from ftp://glycine.nimr.mrc.ac.uk/pub/nige/MView/ as a UNIX gzipped tar archive . This document used to be available at http://mathbio.nimr.mrc.ac.uk/~nbrown/MView/.

Copyright and Licensing

MView and associated libraries are free software, subject to restrictions concerning commercial use. All users must adhere to the licensing terms, acceptance of which is implicit when the software is downloaded.

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. HTML MEDLINE

Maintained by Nigel Brown. Last update Mar 30 1999 .