RT Journal
A1 Raphael, Benjamin
A1 Zhi, Degui
A1 Tang, Haixu
A1 Pevzner, Pavel
T1 A novel method for multiple alignment of sequences with repeated and shuffled elements
JF Genome Research 
JO Genome Research 
YR 2004 
FD November 01 
VO 14 
IS 11 
SP 2336 
OP 2346 
DO 10.1101/gr.2657504 
UL http://genome.cshlp.org/content/14/11/2336.abstract 
AB We describe ABA (A-Bruijn alignment), a new method for multiple alignment of biological sequences. The major difference between ABA and existing multiple alignment methods is that ABA represents an alignment as a directed graph, possibly containing cycles. This representation provides more flexibility than does a traditional alignment matrix or the recently introduced partial order alignment (POA) graph by allowing a larger class of evolutionary relationships between the aligned sequences. Our graph representation is particularly well-suited to the alignment of protein sequences with shuffled and/or repeated domain structure, and allows one to construct multiple alignments of proteins containing (1) domains that are not present in all proteins, (2) domains that are present in different orders in different proteins, and (3) domains that are present in multiple copies in some proteins. In addition, ABA is useful in the alignment of genomic sequences that contain duplications and inversions. We provide several examples illustrating the applications of ABA.