CASIM: Assembly Using Synteny information

[casim]

Is there a program that allows you to use the genome sequences of closely related species to inform the assembly a the genome of a new species, while allowing for a potentially significant loss of synteny

e.g. between two closely related species of bacteria that could have undergone significant rearrangement and gene loss/gain?

[ithersam]

you'll get binding and a PCR product for one allele, but won't get a PCR product for the alternate allele. In practice, non-specific amplification can sometimes make the results difficult to interpret.