Carver AP Biology 5

By dinner time today I will be able to tell you what I want you to do for a grade.  (I'm making up an exercise that will be more meaningful for this unit.)  Meanwhile, feel free to play with the browser, attemp the other exercises, and so on.  I have now fiddled with the thing for hours and have learned a bit by trial-and-error.  Here are some things I have picked up from the tutorial and my experiments.

Understanding the display:

track is wide at exons, half-width are exons at the untrancribed regions (UTRs) at the gene ends (that's how you know you're looking at a whole gene), and narrow lines are introns (with arrow heads showing direction in which the gene is transcribed).

A BLACK track means there exists a corresponding PDB (Protein Data Bank structure) entry for that transcript.  DARK BLUE indicates a reviewed or validated sequence (check info page to see which), while LIGHT BLUE is a non-RefSeq sequence.

The RefSeq track is the original sequence determined, to which others can be compared.  The other tracks are presumably those of other individuals of the same species, or or related partial sequences and RNA transcripts or amino acid sequences.

At the top of the screen is a colored cartoon of the entire chromosome, with a red bar showing where you are in it.  You can go zipping all over the chromosome by clicking where you want to go on this image.  I'm guessing the constriction in the image marks the centromere.

STS sequence tags and SNPs are a single vertical line marking a single site; a wider line is simply closely-spaced STS or SNPs.  (I haven't Googled STS yet.)

Conservation tracks show likely evolutionary relationships as tall bars, while single lines represent gaps where bases don't match up, and double lines indicate more complex situations.

A glance near the bottom of the window shows how the base sequence aligns with a variety of other species, one species at a time.