A novel method for multiple alignment of sequences with repeated and shuffled elements.

TitleA novel method for multiple alignment of sequences with repeated and shuffled elements.
Publication TypeJournal Article
Year of Publication2004
AuthorsRaphael B, Zhi D, Tang H, Pevzner P
JournalGenome Res
Volume14
Issue11
Pagination2336-46
Date Published2004 Nov
ISSN1088-9051
KeywordsAlgorithms, Databases, Genetic, Sequence Alignment, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Software
Abstract

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.

DOI10.1101/gr.2657504
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/15520295?dopt=Abstract
PMCPMC525693
Alternate TitleGenome Res.
PubMed ID15520295