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Nehemiah Wilson
Hello,
I am using your site for my undergraduate research project while I obtain my degree in Biochemistry. I wanted to first figure out how the genomic DNA is represented. Is it the coding strand and listed as 5 prime to 3 prime? Also, I am looking to find out where primers used in previous research fits in the DNA. Is there a feature that would allow me to search DNA and place primers in that sequence?
Thanks,
Nehemiah Wilson
Jonathan Casper
Hello Nehemiah,
Thank you for using the UCSC Genome Browser! Genomic DNA is presented on the forward strand by default, with the 5' end to the left and the 3' end to the right. On many assemblies, an image of the current chromosome is provided above the track display, and your current position within the chromosome is marked in red. Our "Blat" and "In-Silico PCR" tools can be used to locate DNA sequences in an assembly.
You may also be interested in looking at some of the introductory materials we provide on working with the UCSC Genome Browser. Our training page at http://genome.ucsc.edu/training/index.html includes a section with video and written tutorials. The OpenHelix video introduction at http://www.openhelix.com/ucsc provides a nice overview of the tools and configuration options available on our site.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
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Jonathan Casper
Hello Nehemiah,
There are a few additional pieces of information that I should add. First, the reference sequence for chromosomes with centromeres is oriented so that the forward (or +) strand goes from the p arm to the q arm. The reverse (or -) strand goes from q arm to p arm. With regard to your question about coding strand, all genes are displayed regardless of which strand they appear on. There are little arrows ">>>" or "<<<" that indicate the direction of transcription. When the gene has both exons and introns, the arrows appear on the introns (the thin lines between exons). When the gene does not include introns, the arrows appear on the thick block. Here is a session with some custom tracks that show examples of these display styles: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Jonathan%20Casper&hgS_otherUserSessionName=strand_views. Again, the default view is to look at the forward strand (from p arm to q arm). In that view, the ">>>" arrows mean that the gene is on that strand and "<<<" arrows mean that the gene is on the opposite strand. If you would like to see the codons for the reverse strand, the Reverse button below the Browser graphic will reverse-complement everything.
Please note that the strand arrows will only appear when the track is set to "pack" or "full" display mode. More information on display modes can be found in the tutorials and on our help page at http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group