Hi Jeffrey, There are several different ways of determining orthology that won't give the exact same answers. Here's what one of our engineers suggests: Assuming you want to trust the multiz alignments as a best guess at othology, you can use the Table Browser to extract the sequence for any particular gene model and species using the CDS FASTA output option. Please refer to the Table Browser help pages for more information (http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html). This would give you the ACTG's to calculate percentage difference, but keep in mind it will be ignoring inserts and deletes in the other species since the multiz alignments are reference by a single species.
I hope this information is useful and answers your question. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 2/9/2012 10:50 AM, Jeffrey Malone wrote: > Thank you so much for your reply! > > My challenge is that I do not have a large pile of A-T-C-G to compare. I am > currently using the browser and then making comparisions of a human gene > (quite large at 130,542 bp) to other species within the browser using: > > Conservation > Placental Chain/Net > Vertebrate Chain/Net > Primate Chain/Net > Neanderthal Assembly and Analysis > > Unfortunately, these only give colorful bars to compare against the Human > base sequence if I zoom in that far ... but at that level I can only keep > something like 120 bp ... a very far cry from the 130,542. It would be > "possible" to blow everything up and print out more than 1,000 pieces of > paper and start counting ... but I'd prefer another method. > > Starting from the browser ... is there a way that I can do this without > spending the several weeks trying to copy and paste the bits of sequence into > the online BLAT tool? It seems that there must be a way ... but how? > > Thanks again for your help! > > > > > J. Patrick Malone, M.Ed., CVT, LAT-G > Walden University > College of Social and Behavior Sciences > PhD Candidate - Psychology > ID: A00176547 Phone: 541-250-2592 > > > > > --------------------------------------- > Original E-mail > From: Brooke Rhead<[email protected]> > Date: 02/07/2012 03:17 PM > To: Jeffrey Malone<[email protected]> > Subject: Re: [Genome] [BULK] calculating percent difference > > > Hi Patrick, > > Please see this page for citation information: > http://genome.ucsc.edu/cite.html > > There are many ways to calculate a percent difference, and we can't > really advise you on what would be the best method for your purposes. > However, one quick way would be to use BLAT to map the sequence of your > gene to each of the species you wish to compare to: > > http://genome.ucsc.edu/cgi-bin/hgBlat?command=start > > On the results page for each BLAT search, you will usually see several > hits. There is a percent identity calculated for each hit. Keep in > mind that the percent identity only applies to the part of the sequence > that aligns, though. This means that a hit that only aligns in a > section of 20 base pairs can have a percent identity of 100%, if those > 20 bases align perfectly. The score column on the BLAT results page can > help you find the best hit. > > If you have further questions, please contact us again at > [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 2/3/12 8:24 PM, Jeffrey Malone wrote: >> I have enjoyed using the website and will be publishing a paper soon >> in which I would like to site the page. Is there a prefered means >> since so much is a combined effort? >> >> Futher, there is another article I am working on and I wish to make >> direct comparison of the same gene as identified in several species. >> Is there a way to make either a base-by-base calcuation of % >> difference or some other way of obtaining a quantitative account? >> >> Thank you for your wonderful work! >> >> >> >> >> J. Patrick Malone, M.Ed., CVT, LAT-G Walden University College of >> Social and Behavior Sciences Doctoral student - Psychology ID: >> A00176547 Phone: 541-250-2592 >> _______________________________________________ Genome maillist - >> [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
