Question: Aligning Circular Sequences
8
gravatar for William Spooner
9.8 years ago by
Cambridge
William Spooner300 wrote:

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.

alignment • 9.0k views
ADD COMMENTlink modified 2.0 years ago by yaximik0 • written 9.8 years ago by William Spooner300

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.

ADD REPLYlink written 2.0 years ago by yaximik0

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.

ADD REPLYlink written 10 months ago by Jonathanjacobs250
12
gravatar for Lars Juhl Jensen
9.8 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

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.

ADD COMMENTlink modified 9.8 years ago • written 9.8 years ago by Lars Juhl Jensen11k

I like this simple strategy ! :-)

ADD REPLYlink written 9.8 years ago by Pierre Lindenbaum131k

Thomas Down suggested the same via twitter (@dasmoth). I like this approach too.

ADD REPLYlink written 9.8 years ago by William Spooner300
3
gravatar for Pierre Lindenbaum
9.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

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.

ADD COMMENTlink modified 13 months ago by RamRS30k • written 9.8 years ago by Pierre Lindenbaum131k
3
gravatar for Anuraj Nayarisseri
9.8 years ago by
Indore
Anuraj Nayarisseri750 wrote:

Reviewer

Cyclic DNA Sequence Aligner

You can also try out CLC-Bio. which is a very powerful tool.

ADD COMMENTlink modified 13 months ago by RamRS30k • written 9.8 years ago by Anuraj Nayarisseri750
2
gravatar for biobot 0.0.77.a.1099
9.8 years ago by
UK
biobot 0.0.77.a.10996.1k wrote:

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.

ADD COMMENTlink written 9.8 years ago by biobot 0.0.77.a.10996.1k
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