Hello, The general rule is that forward strand is defined as p chromosomal (short) arm -> q chromosomal (long) arm. There are variations on this.
A search brings up the following (among others) that can provide the details: http://en.wikipedia.org/wiki/Centromere http://imgt.cines.fr/textes/IMGTindex/genomicOrientation.html I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] On 7/6/10 5:49 AM, 하승수 wrote: > I'm an undergraduate, and I have finished my courses in biochemistry and > clinical genetics. > Although I'm sure this basic question has been asked and answered several > times before, I cannot form this question into a searchable query that > matches any satisfactory answer neither in google nor this message board so > please forgive me for asking. > > Anyway, my question is this. > > The genome is often presented as a single long string > eg: http://genome.ucsc.edu/cgi-bin/hgGateway > follow the link, press submit, and in the assembly page, press base(right to > zoom in) > or > download a reference genome from > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ > > Lets visualize chromosome number 7 as so, > > chr7.fa > 5' --AAAATTTT-----GGGGCCC>3' : lets call this one A > 3'<-TTTTAAAA-----CCCCGGG5' : and this one B > > Thus, If my understanding is correct, the chr7 can be presented as either > the string that constitutes A or B. Though they are complementary, presented > from 5'->3' they would none the less be different (I checked: chr7 is not > one large palindrome). > > So the genomic strands presented in the above links would can only be A or > B. > (that is, they are either presenting > AAAATTTT -----GGGGCCC(A) or GGGCCCC AAAATTTT(B)) > Lets assume that what we are seeing is A > > *But how is it determined that which of the two should be the one > presented? * > *In other words who chose A over B? Is it just a historical preference?* > * > * > * > * > P.S Sense(antisense) is AFAICT irrelevant here. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
