Entering edit mode
4.8 years ago
awg
•
0
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?
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:
http://multigeneblast.sourceforge.net/
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