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 It also It is distributed under the SuperMap chaining algorithm which is currently unpublished. 1.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. 2. Running Just give it two sequences and let it roll: #slagan 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 (/usr/lib/lagan/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
