Hi,
I am looking for a multiple sequence alignment tool that allows the user to define anchors. That is, the user should be able to define positions in different input sequences that the alignment tool has to align to each other, like: align position 100-105 in sequence A to position 444-449 in sequence B as well as to position 1343-1348 in sequence C.
Does anyone know an MSA tool that offers this feature? There seems to be a version of DIALIGN that is able to do this but I was hoping for a tool that is more established.
So far, I have checked the manuals of the following tools, but without success:
- MAFFT
- MUSCLE
- ProbCons
- Tcoffee
EDIT: It should be mentioned that I need to do this anchoring automatically (i.e. not by editing an alignment by hand) since this problem came up in a project within which a new genome alignment tool is developed.
Are the current results very different around the positions you want to use as anchors? Can you not do this after the fact by (reasonable) editing of the alignment you get?
The reason I cannot do this by hand is that I'm not an end user of alignment software but a bioinformatician who is since recently involved in a project aiming at developing a new genome alignment tool. And it would make things much easier for us if - in a first step - we could identify the mentioned anchors and feed them into an MSA tool which can handle them.
You may want to add this information to the original post by editing since it is an important consideration for you.