-=- run-mummer1 (MUMmer1.0) README -=-

** NOTE **
This manual is outdated, please refer to the HTML documentation included in
this distribution or at:

   http://mummer.sourceforge.net
   http://mummer.sourceforge.net/manual
   http://mummer.sourceforge.net/examples

This is the README for the original MUMmer 1.0 system, which is
included in the MUMmer 3 package.  It is slower and uses more memory,
but it does have some slightly different functions and output so we
make it available.  



MUMmer 1.0 code and documentation are copyright (c) 1999 by The Institute
for Genomic Research.  The principle architect for the system was
Arthur Delcher.

This directory contains the source code for MUMmer program for
aligning long DNA sequences.  If you use this code in any publication,
please cite the following:
   A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson,
   O. White, and S.L. Salzberg.  Alignment of whole genomes.
   Nucleic Acids Research, 27:11 (1999), 2369-2376.

MUMmer works on Unix only.  This README file is the only documentation
besides the code itself.  Since it is free, we cannot provide any
other support.  The system is very easy to use, but you need to invest
a few minutes up front reading this file and figuring out how to
interpret the output.  If you discover bugs, we would be interested in
hearing about them so we can correct them.  Address bug reports to
<mummer-help@lists.sourceforge.net>. The system uses a LOT of RAM - if
it crashes for that reason, that's not a bug.  We recommend at least
512Mb to align most pairs of bacterial genomes, and 1Gb or more may be
required.

To use this system, first compile it by typing 'make' at the
command line.  There is a script, 'run-mummer1', that runs all
the steps of aligning two genomes.  The script takes these arguments:

     run-mummer1 <genome1> <genome2> <tag> [-r]

The two genomes must DNA sequences in FASTA format.  Multi-FASTA
files don't work.  The tag is used to create 4 output files,
all with 'tag' as a prefix.  -flip  will reverse complement <genome2>.

Of the four output files, two are intended for your inspection.
<tag>.errorsgaps lists the alignment of all the MUMs (maximal unique
matches - read the paper for definitions), and includes the longest
ascending sequence of MUMs first.  This sequence is the best alignment
of the two genomes by the program.  In between the MUMs are gaps,
which are aligned using a Smith-Waterman implementation of our own.
Those Smith-Waterman's are contained in the file <tag>.align.
This can be a very long file if there are lots of gaps.  If either
of the two gaps is too long (over 5000bp), then the alignment is
not performed.

IMPORTANT: the performance of the program can critically depend on the
minimum MUM length you use.  The default is 20bp.  If you want to 
change it, do the following:  edit the file run-mummer1. Add a new
length switch to the 'mummer' call.

The other file - one that we often spend lots of time analyzing - is
<tag>.errorsgaps.  The lines in that file are the MUMs, for example:
   46989   271588     23    none   3262   3304    1022
   47013   271612     24    none      1      1       1
Columns 1 and 2 are the positions of a MUM in genomes 1 and 2.  The
MUM is 24bp in length, shown in column 3.  Column 4 is the overlap
from the previous MUM - usually this will be 'none' except when there
are repeats present.  Columns 5 and 6 show the gaps from the *end*
of the previous MUM.  Column 7 shows the number of errors - indels
or mismatches - in the S-W alignment of the gap before this MUM.
Hence in the two lines shown here, the second line is a MUM of 24bp,
and it follows the previous MUM after a gap of just 1bp in each genome.
This indicates a single nucleotide polymorphism.

Files in this directory:

   annotate.cc  Adds alignment info to gaps file produced by  gaps
     or  gaps2 .  Reads frag info from the file named on the '>'
     lines of the gap file.  The word "reverse" after that name
     will make that sequence get reverse-complemented.
     Also produces file  witherrors.gaps  which is the same as the
     gaps input file, put with an extra column of number of
     errors.

   gaps.cc  Finds longest consistent set of matches in list
     produced by mummer1 program.

   run-mummer1  Script to run alignment programs.  Format is:
     run-mummer1 <genome1> <genome2> <tag> [-flip]
     <tag> will be used to make output files:  <tag>.out , <tag>.gaps
     and  <tag>.align .  -r  will reverse complement <genome2>

Email questions, comments or bug reports to: <mummer-help@lists.sourceforge.net>

