[ANNOUNCE] MView 1.41: html alignments from blast/fasta/other

Nigel Brown nbrown at lysine.nimr.mrc.ac.uk
Thu Apr 29 08:18:59 EST 1999


MView, release 1.41

    http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/
    ftp://glycine.nimr.mrc.ac.uk/pub/nige/MView/

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 coloured Web
page from a BLAST or FASTA search complete with scoring information, or
from a CLUSTAL alignment allowing quick assessment in a Web browser in
terms of sequence conservation patterns. It can also be used as a format
converter.

----

  Changes in this release include:

   o Limited GCG 9.1 support with FASTA and BLASTP parsers.
   o FASTA3 parser handles query strand orientations.
   o Row filtering extended to allow regular expressions.
   o Use of a reference row can be switched off completely.
   o Smaller output files with Cascading Style Sheets.
   o Better memory use.
  
----

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.

Currently recognised input formats include:

  NCBI BLAST (2.0 series)
     blastp, blastn, blastx, tblastn, tblastx, psi-blast
  
  NCBI BLAST (1.4 series)
     blastp, blastn, blastx, tblastn, tblastx
  
  WashU BLAST2 (2.0)
     blastp, blastn, blastx, tblastn, tblastx
  
  FASTA (3.0 series)
     fasta3, tfastx3
  
  FASTA (2.0 series)
     fasta, tfastx
  
  MaxHom/HSSP
  
  and the following flatfile formats:
     Pearson, PIR, MSF, CLUSTAL

Alternative output formats are also supported: plain text, Pearson, PIR,
and MSF, for export to other programs. See the Web page for the most recent
information.

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

See: http://mathbio.nimr.mrc.ac.uk/~nbrown/MView/
     ftp://glycine.nimr.mrc.ac.uk/pub/nige/MView/

for details and instructions, and also the (very out of date) article:

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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 Nigel P. Brown,                                     nbrown at nimr.mrc.ac.uk
 http://mathbio.nimr.mrc.ac.uk/~nbrown/                                   
 National Institute for Medical Research,         Tel: +44 (0)181 959 3666
 The Ridgeway, Mill Hill, London NW7 1AA, UK      FAX: +44 (0)181 913 8545
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