I need to do an alignment of two bacterial E. coli strain genomes (~4.5 Mb each), preferably with the ability to annotate the divergent regions. I typically use Invitrogen's Vector NTI software suite for working on smaller circles (<10 kb) but have found that the software doesn't seem to be designed to manage anything to the scale of an entire genome.
I've looked at MUMmer but since we have no Linux machines in this lab I'm a bit limited there. (Running Windows XP Pro on all our machines--small operation).
Is there an open source equivalent of something like Roche's gsMapper available?
I've looked at MUMmer but since we have no Linux machines in this lab I'm a bit limited there. (Running Windows XP Pro on all our machines--small operation).
Is there an open source equivalent of something like Roche's gsMapper available?
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