Hi Ariel, LiftOver uses genomic similarity as generated by the Chain track. Unique/specific genomic similarity (synteny) can help confirm an ortholog, especially between evolutionarily close species. That said, using a transcript in genePred format and running a liftOver is a choice - but evaluate manually for scientific integrity - and consider a reverse liftOver to accomplish a "reciprocal best hit" methodology. Will work for some, but certainly not for all. Your experience with the similiarity between these two genomes can help guide you about whether this is something worth trying or not. It is certainly a worth investigating.
As you know, any bioinformatics analysis is highly dependent on genome quality, transcript quality, and other factors such as correctly masking repeats (or not). Example of a complicated case: the functionality is accomplished by one gene in species A but by two genes in species B or there are multiple simliar copies in species B, the result of duplication - all along the same stretch of genomic interspersed with varients that act as regulators or psuedogenes not selected against yet (or performing a function not characterized yet). The point is that running a large number of genes in batch and trusting the output will not provide what you are looking for. If you want to start with genomic similarity then track back to genes, the Conservation track in D. melanogaster would be a good place to start. If you really wan to use liftOver, the suggestions is to run a few experiments using the hgLiftOver tool and load results back into browser as a custom track to evaluate in the context of the entire genome & associated annotation. http://genome.ucsc.edu/cgi-bin/hgLiftOver Good luck and if you need help finding specific FAQ documents or have parameter questions, just let us know, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Ariel Paulson" <[email protected]> wrote: > From: "Ariel Paulson" <[email protected]> > To: [email protected] > Sent: Friday, August 21, 2009 12:30:34 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] LiftOver and ortholog mapping > > Hi, > > Superficially, it seems that liftOver might be a good way to do > ortholog identification, especially for closely related species like > D. melanogaster and D. yakuba. Does anyone know if this is NOT a good > idea in theory/practice? > > Thanks, > Ariel > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
