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Circular sequence comparison

Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques. As circular molecular structure is a common phenomenon in nature, a caveat of the adaptation of alignment techniques for circular sequence comparison is that they are computationally expensive, requiring from super-quadratic to cubic time in the length of the sequences.

This tool is used for alignments of sets of circular DNA/RNA; If the input sequence are RNAs, please replace the 'U' with 'T' first.

1. Enter set of FASTA sequence(DNA/RNA,no more than 100 sequences,no exceeds 1MB):

Sequence Number:0

Sequence Length:0

2. Output format:

3. Sequence type:

4. If color the output:

Circular DNA

Circular DNA is DNA that forms a closed loop and has no ends. Examples include: Plasmids, mobile genetic elements; cccDNA, formed by some viruses inside cell nuclei; Circular bacterial chromosomes; Mitochondrial DNA (mtDNA); Chloroplast DNA (cpDNA), and that of other plastids; Extrachromosomal circular DNA (eccDNA).


Grossi, R., Iliopoulos, C.S., Mercas, R. et al. Circular sequence comparison: algorithms and applications. Algorithms Mol Biol 11, 12 (2016).