Aubergene readme.txt, $Revision: 1.1 $$Date: 2006/02/07 13:36:51 $

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Run the main program with

	python transali.py
	
to see the list of options.

The program uses BLASTZ format to write and read alignments
(see http://www.bx.psu.edu/miller_lab). In the original alignment,
each segment has assigned a score together with percent identity. 
Aubergene uses the identity field to report the number of 
"confirmations" from transitive alignment (ranging between
1 and the number of intermediate genomic sequences). This value
can be optionally rescalled to 100 (see -n option).

Example:

	python transali.py -m -d -i -n human mouse dog cat .blastz

will create human-dog-mouse human-cat-mouse transitive alignments.
To create the transitive alignment, the following files will be used:

	human_dog.blastz dog_mouse.blastz
	human_cat.blastz cat_mouse.blastz
	
Sometimes (e.g. when -d option is not used) the direct alignment 

	human_mouse.blastz
	
will be read as well.


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A small tool, regionsalign.py, is present in this directory. The purpose 
of this utility is, among others, to intersect an alignment with
a given region (for example, known exons), filter the collective 
aligment while keeping only matches which were confirmed by at 
least k transitive alignments, or print the number of residues 
covered by alignment in the given region. Run

	python regionsalign.py
	
to see the list of options.

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Please cite 

	Szklarczyk, R., Heringa, J., AuberGene - a sensitive genome alignment tool,
	Bioinformatics, 2006 (accepted)

when you use this material.

Radek Szklarczyk
radek@cs.vu.nl

Vrije University Amsterdam
De Boelelaan 1081
1081HV Amsterdam
The Netherlands

Tel: +31 20 598 78 43
Fax: +31 20 598 76 53