Question: Alignment algorithm for unordered blocks or domains
gravatar for tonygoering
4 weeks ago by
tonygoering0 wrote:

On the MAFFT website there is a "merits and limitations" section. I found the third limitation interesting: "3. The order of alignable blocks or domains are assumed to be conserved for all input sequences."

What are some examples of programs or tools that are build to solve this problem?

What would you use to align sequences that may include blocks or whole sections that are in a different order?

alignment • 73 views
ADD COMMENTlink written 4 weeks ago by tonygoering0

I'm not sure if this is exactly what you're looking for, since this is for multiple genes, rather than multiple segments of a gene, but conceptually its the same thing:

ADD REPLYlink written 4 weeks ago by jrj.healey13k

perhaps something like DIALIGN-TX might be useful.

are we talking proteins here btw? long shot but some tools for promoter element detection work on conserved alignment and do allow order of motifs to change between sequences

ADD REPLYlink written 4 weeks ago by lieven.sterck5.5k
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