Concatenating Bacteria Genome Contigs

Question

[robjohn7000]

Hi,

Is it a good idea to concatenate contigs for doing comparative genome analysis? Any suggestions for the correct approach will be appreciated.

Thanks

Answer 1

[Lee Katz]

It's not always a great idea, but you can do it. If you do concatenate, the best idea is to concatenate with artificial linker sequences. For example if you are looking at genes on these contigs, you want to start and stop the genes that run off the edges. You can start/stop them using a sequence with start and stop codons in every frame.

[robjohn7000]

Many thanks Lee.