Hello Jamie, In terms of measuring conservation you'd be better off using the phastCons or phastOdds tracks since they use the same alignment that the protein FASTA does but analyze it in the context of the whole genome. For information about those tables try searching for "phastCons" or "phastOdds" on our mailing list accessible here:
http://genome.ucsc.edu/contacts.html With respect to the predicted amino acid sequence in other species, there has been no attempt to compare these sequences with native protein sequences from the animals in question. Unfortunately this would be impossible for the large majority of proteins since human is so much better annotated that other species, and even in human, the protein product for most predicted genes hasn't been confirmed experimentally. I know of no publications that explicitly use the protein FASTA prediction files per se, but a large number of publications have referenced the UCSC multiple alignments which have included codon translation for other species for many years now. Try searching for "ucsc genome browser multiple alignment" at PubMed. I hope this gets you started on exploring the UCSC genome browser multiple alignments and downstream conservation analysis. Please send mail to this list again if you have more questions after exploring the resources I mentioned. Brian Raney On Thu, Sep 24, 2009 at 11:25 AM, Kapplinger, Jamie D. < [email protected]> wrote: > Hello, > > I am hoping to use the protein FASTA to be able to determine > conservation across species. I understand that this is based off a > genomic alignment for the species listed. So I was wondering whether > there has been a comparison for the Protein FASTA amino acid sequence > provided by UCSC to the accepted amino acid sequence for each species to > determine how accurate this genomic derived sequence is? If you could > point me to any publications using the UCSC protein FASTA it would also > be appreciated. > > Thanks. > > Jamie Kapplinger > Research Technologist I > Windland Smith Rice > Sudden Death Genomics Laboratory > Phone: (507) 538-7321 > Fax: (507) 284-3757 > E-mail: [email protected] <mailto:[email protected]> > ______________________________ > Mayo Clinic > 505 Guggenheim > 200 first Street SW > Rochester, MN 55905 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
