Hello Suganthi, The general answer is no, if the alignment is +/- then that is the data to compare. If human is + strand and the others are - strand in the multiple alignment, that means that was the best fit for the entire region. For this position, the G in the human reference genoese on the + strand is directly comparable to the orangutan/macaque G on the - strand. Possibly some rearrangement has occurred. Look at the surrounding data to interpret in the context.
The alignments are produced using multiZ and are based on the best fit for entire blocks of genomic sequence. The advice to interpret the surrounding sequence of this position to determine which strands in human and the other species are a match. For most cases, this be the strand as shown in the browser (as produced by multiZ). Consider this alignment a starting place, then use your own knowledge to interpret the results and (potentially) discover reasonable alternative alignments. And yes, for any genome, it would be expected that the opposite strand at any single position would have the expected complimentary nucleotide. This is what the reference genome will contain. However, in the actual genomic sequence itself, this rule could be broken and could be an area of interest for variation and may be the content presented in some tracks with variation data. I hope this helps, Jen ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Su Bal" <[email protected]> wrote: > From: "Su Bal" <[email protected]> > To: [email protected] > Sent: Wednesday, January 27, 2010 10:36:31 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Ancestral allele information from table browser > > Hi, > > I have a quick question about how to interpret the fields when I used > the > Table browser to obtain ancestral allele information. I think it will > be > easiest if I explain my problem with an example > > For dbSNP rs11040198, > I understand that the human and chimp allele are G on the positive > strand. > For orangutan and macaque, the "G" allele is on the negative strand. > Does > this mean that for orangutan and macaque actually have "C'" at the > +ve > strand. I am not sure how to use the strand information to figure out > how > they are comparable to each other. My reading of this would be that > human > and chimp have the same allele, G, at that position, but orangutan > and > macaque have a C. Am I correct? Thanks for your help. > > Best, > Suganthi > > Suganthi Balasubramanian > Associate Research Scientist > Yale University > CT 06520 > USA > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
