Genome alignment/analysis question

[jvntc]

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?

[-daf-]

look at Mauve

http://gel.ahabs.wisc.edu/mauve/

Aaron C.E. Darling, Bob Mau, Frederick R. Blatter, and Nicole T. Perna. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research.

[aphillippy]

Also, look into Cygwin (http://www.cygwin.com) if you want to run Linux programs from XP. It will provide you an emulated linux environment for building ifx tools like MUMmer that aren't released as a windows binary.