Comparing two or more genomes for novel regions

Question

[dr_mm_sh]

Usually blast search looks for similarities. How about looking for unique regions among several genomes. Is it possible? How to do it? I found the pan-seq to find novel regions among bacteria. How about fungi or plant? Any advice for a windows user? Thanks in advance.

Answer 1

[Chrispin Chaguza]

You could use ACT to compare multiple genomes (or genomic regions) to identify unique regions. You could also use OrthoMCL to identify unique regions (genes) in your species genomes.

Here is an example of how genome comparisons by ACT look like http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648787/figure/F3/

[dr_mm_sh]

Thanks Chrispin Chaguza for your kind advice. I tried to use ACT but I always got an error message that is

error while reading: End of file while reading from: \20113[1..30220833](2).flat

The latter is the comparison file that I produced using blast.

Any suggestions?