[ANNOUNCE] MView 1.37: extract alignments from blast/fasta/other

Nigel Brown nbrown at lysine.nimr.mrc.ac.uk
Thu Oct 15 15:14:38 EST 1998


MView, release 1.37

    http://mathbio.nimr.mrc.ac.uk/nbrown/mview/     **Note NEW URL**

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 colorized Web
page from a BLAST or FASTA search allowing quick assessment of the hits in
terms of sequence conservation patterns alongside the scoring information.

----

  Changes in this release include:

   o Extension to the full BLAST suite of programs, notably tblastn by
     popular demand.
   o Column names added to numeric fields (score, expect, etc) for search
     programs in BLAST/FASTA suites.
   o Limited control from command line allowing a subrange of alignment
     columns to be extracted and displayed.
   o Semi-automatic input format detection based on filename or extension and
     specific program/version of BLAST or FASTA suite determined
     automatically. 
  
  Bug fixes:

   o Ordering of HSPs in reverse complemented query strands was wrong for
     blastn (series 1.4).
   o More efficient memory usage.

----

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

Currently recognised input formats include (*=new):

  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/ for details and
ftp/installation instructions, and also the 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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