Hi,

have a look at this site, you can find different kinds of sequence alignments (global/local/genomic alignment)

http://www.ebi.ac.uk/Tools/psa/

good work

Thank you!

As others have stated this is not necessarily a trivial task, especially as you do not say how close the organisms are; aligning strains of the same species or two distinct species? Whether these are from prokaryotes or eukaryotes makes a big difference as well. I'm assuming these to be closely related bacteria genomes.

My suggestion would be to run a simple alignment and then visualise using ACT (http://www.sanger.ac.uk/resources/software/act/). You may want to define syntenic regions not at the DNA level but by protein-coding genes which greatly reduces the complexity of the problem and reduces noise in the alignments to really see the differences between the two genome assemblies (with the caveat that this is gene centric and will not show you differences in repeats or non-genic sequence motifs).

Why not do a gene:gene comparison, looking for genes in common between the two (and yes, the trick is identifying those by homology), then do alignments for each matched set, and come up with a metric that involves both a global similarity of shared genes as well as similarity within genes? It gets, well, fiddly, as you look at the range of conservation within genes, but it is at least a tractable approach. Gene order of course could be thrown into the mix, although without throwing more species into the comparison that wouldn't be terribly telling.

BLAT is a pretty reasonable way to do this. It is quite fast and give a pretty simple output. I guess it all comes down to your genomes... how big are they?

Perform alignment with dotplot method, it will give you multiple directions

The dot plot technique is not easy if the genomes are big. You may use Mauve software that combine BLAST and DOT plot (globally)

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

The genomes have to be enough close for the MAUVE or Dotplot.

If the genome sequence are divergent you could translate all the putative proteins and make a dotplot with all the concatenated proteins

Thank you all!

I have 2 genomes...Same species and different strains. It is really close but have little differences between. I want to compute/show this differences.

By the way the genomes have approximately 9.000.000 pb each.

Mauve is the best for determinate colinearity and deletion/insertion

For genome genome comparison MUMMER is a very good software which gives pretty good results. Then you can even visualize your results with ACT which will show you the differences between two genomes in term of insertion, deletion etc.