AliWABA is a website and portal for ABA, the A-Bruijn Aligner described in:

A Novel Method for Multiple Alignment of Sequences with Repeated and Shuffled Elements.
Benjamin Raphael, Degui Zhi, Haixu Tang, and Pavel Pevzner.
Genome Research (2004) 14,(11)2336-46. (BibTeX)

There are two ways to run ABA.

• You may use our online version. (Recommended)
• You may download the ABA software
.

When ABA is applied to repeat libraries, including those generated by the RepeatScout libraries, we observe a number of interesting things that are described in the paper below. You may view the connected components of ABA run on the Human RepBase libraries directly, but due to licensing restrictions on RepBase Update we cannot make the sequences available from this website. Nor can we provide an automatic way of importing repeats into the online ABA software.

Identifying Repeat Domains in Large Genomes.
Degui Zhi, Benjamin Raphael, Alkes Price, Haixu Tang, and Pavel Pevzner.
Genome Biology 2006 7,(1):R7. (BibTeX)