MSPcrunch / Blixem  README
==========================

This directory contains MSPcrunch, Blixem and various other tools for
improving database searching with Blast.

  Files:

  =README                 This file
  MSPcrunch.LIN           MSPcrunch for Linux
  MSPcrunch.OSF.Z         MSPcrunch for DEC Alpha OSF/1
  MSPcrunch.SGI.Z         MSPcrunch for Irix
  MSPcrunch.SUN.Z         MSPcrunch for SunOS
  MSPcrunch_source.tar.Z  MSPcrunch source code
  MSPcrunch2.ps.Z         Postscript file on MSPcrunch version 2.0 (22 pages)
  blixem.OSF.Z            Blixem for DEC Alpha OSF/1
  blixem.SGI.Z            Blixem for Irix
  blixem.SUN.Z            Blixem for SunOS
  blx                     Script to call MSPcrunch and Blixem in one go.
  TESTS.tar.Z             Some test examples.
  efetch.tar.Z            Efetch program to retrieve sequence entries from databases
  seqsplit.tar.Z          Package of query-splitting and -unsplitting programs
  BLOSUM62-12             Modified Blosum62 for high-quality DNA sequences


This is a rough sketch of how some of the programs fit together:


BLAST -> MSPcrunch -> BLIXEM

                        ^
                        |
                      Efetch
                        |

                    <databases>


The script blx makes the user interface more friendly by calling
MSPcrunch and Blixem the proper way.

The latest documentation of MSPcrunch is provided in the file
MSPcrunch2.ps.Z.  Blixem and an old version of MSPcrunch are described
in "Sonnhammer and Durbin (1994) A Workbench for large-scale sequence
homology analysis. CABIOS 10:301-307".  A more recent paper on
MSPcrunch is described in "Sonnhammer and Durbin (1994) An expert
system for processing sequence homology data. Proceedings of ISMB 94,
363-368".  Efetch is only required to retrieve annotation on-the-fly
from databases. See the README in efetch.tar.Z.


INSTALLATION

FTP, uncompress and untar if necessary the files you need.  Rename to
blixem and MSPcrunch and chmod 777.  If you have a query sequence in
fasta format in the file 'myseq', and your X-terminal is called
'myterm', do the following to view the relevant blast matches in
Blixem:


1. Make sure blixem, MSPcrunch and blx are in your path.

2. setenv DISPLAY myterm:0

3. Run blast either locally or by Email (blast@ncbi.nlm.nih.gov).
   For BLAST 1.3, use the parameters described in the CABIOS paper,
   but for BLAST 1.4 and WUBLAST you're better off with the parameters
   described in the file MSPcrunch2.ps.Z.
   Save the blast output in the file 'myseq.blast'.

4. blx myseq myseq.blast

This should give you a blixem alignment of your blast output, which is
what most novice users want.  More advanced users should know that
MSPcrunch has many options and is also a very useful program in its
own right even without Blixem. See the references above for more info.
Typing only MSPcrunch or blixem will give a brief help.


To get source for blixem, get source from
ftp://ftp.sanger.ac.uk/pub/acedb
and do "make blixem"

If you have any problems, please Email me.

Erik.Sonnhammer@scilifelab.se
2014-04-25