Cyclic DNA Sequence Aligner


This tool finds the optimal rotation for a set of circular DNA sequences that are going to be aligned. It is very well suited to apply to mitochondrial genome alignments, and also for plasmids, chloroplasts, circular viruses and bacterial chromosomes.

The best rotation is calculated based on the longest chain of non-repeated blocks that belongs to all the sequences. These maximum common blocks are obtained with the help of a generalized cyclic suffix tree data structure.

As of yet, the current version of this tool does not perform the multiple sequence alignment itself. But some suggestions of other highly efficient multiple sequence alignment tools to perform this task are presented on the right.


The sequences can be submitted in Multi-FASTA format by uploading a file or by copying/pasting the sequences in the text window. There is a limit of 64 sequences and 5 MB per file.



User Manual


Source code
Example sequences
Use 'unzip' to unpack and 'make' to compile.
Run with: CSA R sequences.fasta


Fernandes F., Pereira L., Freitas A.T.:
CSA - An efficient algorithm to improve circular DNA multiple alignment.
BMC Bioinformatics, 2009, 10:230.


Please send your comments, suggestions, bug reports or questions to: