Hello Fahad, Questions concerning use of the Genome Browser can be addressed to [email protected] (no need to send to the genome-mirror address).
For basic biology questions, I suggest consulting wikipedia, for instance, this page: http://en.wikipedia.org/wiki/Sense_(molecular_biology) I assume you are using BLAT (http://genome.ucsc.edu/cgi-bin/hgBlat) to align the mutated CTSG gene to the reference genome. Reversing the view of the gene in the Genome Browser has no effect on BLAT searches -- the positive and negative strands are both searched for matching sequence. So, you can copy and paste your sequence into the BLAT search window, hit submit, and then click the top "browser" link to see the alignment in the Genome Browser. If your sequence aligned to the negative strand, you will see arrows going to the left (<<<) in the "normal" view, or going to the right (>>>) in "reverse" view. Bases that differ from the reference genome will appear as red lines in your alignment, and insertions or deletions will appear as orange lines. I hope this is helpful. If you have further questions, please feel free to write back to the genome mailing list. -- Brooke Rhead UCSC Genome Bioinformatics Group Fahad Hakami wrote on 12/26/09 12:47 PM: > > > Dear Sir/Madam, > > > > I have few urgent question that I became tired of looking for there answers!! > > > > What is the difference between a gene located on the - strand, like CTSG gene, and a gene located on the + strand, like NFATC4?? > > > > Which one is called sense, comlementary, template oriented?? > > > > What is the diffrence between there mRNA?? and how their mRNA are synthesised ( I mean from which strand )? > > > > In case of CTSG gene: If I want to make an alignment of its exons > with a sequence that have a mutation, should I do this alignmnet while it is in the - strand direction or I have to reverse it on the browser then do the alignmnet?? > > (the next step will be checking which amino acid will be synthesized instead of the reference one) > > > > Please I beg you, answer me as soon as possible. > > > > Yours, > > > > Fahad > > _________________________________________________________________ > Hotmail: Powerful Free email with security by Microsoft. > http://clk.atdmt.com/GBL/go/171222986/direct/01/ > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
