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Shuffle-LAGAN with SuperMap README
Michael Brudno, brudno@cs.toronto.edu
0. Overview
This directory contains the code for Shuffle-LAGAN, a glocal alignment tool described
in Brudno, Malde, Poliakov, Do, Couronee, Dubchak & Batzoglou "Glocal alignment: Finding
rearrangements during alignment", ISMB 2003 Proceedings (see
http://lagan.stanford.edu/cite.html for detailed citation information).
It also
It is distributed under the SuperMap chaining algorithm which is currently
unpublished.
1. Installation
If you received Shuffle-LAGAN as part of the LAGAN toolkit it is installed
automatically with the rest of the package. The code assumes $LAGAN_DIR
has been set.
2. Running
Just give it two sequences and let it roll:
#slagan.pl seq1.fa seq2.fa
3. Input
The input sequences should be in FASTA format. You should provide a
.masked file for each of the sequences (see README.FIRST) Output will be
in XMFA format, described lower.
4. Output
The overall result are three files, a .chaos file with the local
alignments in the chaos format, a .mon file with the 1-monotonic chain
(see http://lagan.stanford.edu/manual.html for what this is) and a .xmfa
file with the actual alignments in the XMFA format.
A. XMFA Format
The format is based on Multi-FASTA, but allows for several multiple local alignments to be
stored in a file. It is as follows:
> seq_num:start1-end1 +/- comments (sequence name, etc.)
AC-TG-NAC--TG
AC-TG-NACTGTG
...
> seq_num:startN-endN +/- comments (sequence name, etc.)
AC-TG-NAC--TG
AC-TG-NACTGTG
...
= (line starting with an "=" separates different alignments, and can have any comments)
> seq_num:start1-end1 +/- comments (sequence name, etc.)
AC-TG-NAC--TG
AC-TG-NACTGTG
...
> seq_num:startN-endN +/- comments (sequence name, etc.)
AC-TG-NAC--TG
AC-TG-NACTGTG
...
5. Parameters
Will be described for the next release. E-mail the author for details.
6. Utilities
The utilities directory ($LAGAN_DIR/utils) has 2 programs which may be of
use to Shuffle-LAGAN users:
A. Glue
Given a Shuffle-LAGAN alignment in XMFA format it glues together a "fake"
second sequence and builds a single pairwise alignment in multi-fasta
format. This can then be visualized using VISTA, or used in other ways
(e.g. you can get several of these "fake" sequence and use MLAGAN to do
multiple alignment).
B. dotplot
Given a list of local alignments in the format of the monotinic file
(.mon) it builds a series of gnuplot commands that build a dotplot of the
local alignments. Useful for seeing which rearrangements were found.
This README will be extended in the future.
Please send questions to Michael Brudno, brudno@cs.stanford.edu
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