Aligning Circular Sequences
4
8
Entering edit mode
11.0 years ago

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 • 10k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
12
Entering edit mode
11.0 years ago

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 COMMENT
0
Entering edit mode

I like this simple strategy ! :-)

ADD REPLY
0
Entering edit mode

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

ADD REPLY
3
Entering edit mode
11.0 years ago

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 COMMENT
3
Entering edit mode
11.0 years ago

Reviewer

Cyclic DNA Sequence Aligner

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

ADD COMMENT
2
Entering edit mode
11.0 years ago

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 COMMENT

Login before adding your answer.

Traffic: 1593 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6