The BioInformer nr. 4, 1998 --- Mview alignment viewer




	A publication of EMBL - Outstation Hinxton, The European Bioinformatics Institute

MView, release 1.36

MView is a free tool for converting the results of a sequence database search into the form of a multiple alignment of hits stacked against the query. For completeness, existing multiple alignments can be post-processed in the same way. A typical application is the generation of a colorised Web page from a BLAST or FASTA search allowing quick assessment of the hits in terms of sequence conservation patterns alongside the scoring information.

Currently recognised input formats include: FASTA, TFASTX, BLASTP, BLASTP(WashU), BLAST2, PSI-BLAST, BLASTN, BLASTN(WashU), Pearson, PIR, MSF, CLUSTAL, MaxHom/HSSP, but see the Web page for the most recent information.

Alternative output formats are also supported: plain text, Pearson/FASTA, PIR, and MSF, for export to other programs.

Example output for the PP2C superfamily derived from a hand finished clustalw alignment. Click for an enlargement.

MView allows filtering of the input by score, e-value thresholds, psi-blast search cycle, etc., provides a choice of colouring schemes and palettes for protein or nucleotide sequences, and can generate consensus patterns.

This software requires Perl (version 5) and runs on UNIX systems.

Availability

MView can be downloaded and used for free, but users should familiarise themselves with the copyright restrictions.

Information by: Nigel Brown

Resources and further information

MRC National Institute for Medical Research
http://www.nimr.mrc.ac.uk/

Division of Mathematical Biology
http://mathbio.nimr.mrc.ac.uk/

MView homepage
http://mathbio.nimr.mrc.ac.uk/nbrown/mview/

Download MView
ftp://glycine.nimr.mrc.ac.uk/pub/nige/MView/

Nigel Brown´s homepage
http://mathbio.nimr.mrc.ac.uk/~nbrown/

Literature:

Brown, N.P., Leroy C., Sander C. (1998). MView: A Web compatible database search or multiple alignment viewer. Bioinformatics. 14(4):380-381.

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Direct questions or comments to Bioinformer Editor. This page last modified Friday, 16 July, 1999.
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