I have a 20K plasmid that I want to align to a plasmid database. I don't know the origin of my query sequence relative to the target. Does anyone know of a circular-aware aligner? Either global or local would be fine.
There is a very simple way to circumvent the problem of not knowing the origin. What you can do is to make a sequence that consists of two concatenated copied of your plasmid, and then align this against the plasmid database using a normal alignment program (e.g. BLAST). No matter where the origin is, it will be able to produce full-length alignments.
I found this one, using pubmed: Cyclic DNA Sequence Aligner
This tool finds the correct rotation for a set of circular sequences that are to be aligned. It is very well suitable for example to apply to mitochondrial genome alignments.
The best rotation is calculated based on the largest 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.
As it is developed, this tool does not perform the multiple sequence alignment itself. The user is presented with some suggestions of other highly efficient multiple sequence alignment tools to perform this task.
You can also try out CLC-Bio. which is a very powerful tool.
I've heard of circal, but haven't used it. The paper links to the source code.
The only other thing I know of that comes close is Cyclic DNA Aligner described in this paper. However, this is a preprocessor not an aligner.
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CLC-Bio Genomic Workbench does not seem to be aware for alignment purposes if sequence is circular. Although it can show rCRS mtDNA as circular, it cannot properly align to it a linear sequence that is should align between pos. 16022-origin-1280. Nor can Geneious, for another example.
Just as an FYI - This is actually not the case with CLC. The CLC read mapper, aligner, and multiple sequence alignment tools indeed support aligning circularized sequences or (in the case of read mapping NGS data) correctly mapping to a circular reference. In addition - the ability to set fixpoints in an alignment provides a very high level of control over the alignment algos as well.