I am posting emailed questions and my answers here with the idea others may benefit.
Issues
In trying out my own instructions to recreate a student's problem, I found I didn't get the same search results I did the first time--not sure why, but here's the fix: if searching for "rna polymerase" doesn't get the results I describe, search "dna-directed rna polymerase" instead. When I did so, "dna-directed rna polymerase II A" appeared third in the list. Proceed from there.
Questions and Answers
"I cannot seem to zoom in to see the single nucleotides. Either that or I just don't know what they look like."
Note that there are two sets of zoom buttons: one for zooming in, one out. When I called up dna-directed rna polymerase II A, I found that clicking 10X twice got me the amino acid sequence, but not the base sequence. An additional push of 1.5X got me bases. They are caps right under the position number line at the top of the window. Alternatively, push the "Bases" button to get directly there, with the center of the sequence shown. I like using the zoom buttons better since they give me a more intuitive sense of the scale of things, and how big the total sequence must be.
When doing the assignment is it normal to get a lower score from the BLAT comparing to the base pairs to the chicken genome than comparing them to the lancelet genome?
I don't know about "normal"--it just is what it is! I confess to being surprised myself. (Think about why this might be surprising!) One thing I learned poking around the "Homology" entry in Wikipedia last night (and no, I don't turn up my nose at Wikipedia) is that some level of matching between genes in different species is not "proof" that these genes descended from a common ancestor. In other words, the bigger score for the lancelet may be a coincidence. I just don't know. Of course, I'm just a teacher and not a scientist, but one of the cool things about this software is that we might just be doing REAL SCIENCE. It's a big universe in there, and NO ONE knows all the answers!
Issues
In trying out my own instructions to recreate a student's problem, I found I didn't get the same search results I did the first time--not sure why, but here's the fix: if searching for "rna polymerase" doesn't get the results I describe, search "dna-directed rna polymerase" instead. When I did so, "dna-directed rna polymerase II A" appeared third in the list. Proceed from there.
Questions and Answers
"I cannot seem to zoom in to see the single nucleotides. Either that or I just don't know what they look like."
Note that there are two sets of zoom buttons: one for zooming in, one out. When I called up dna-directed rna polymerase II A, I found that clicking 10X twice got me the amino acid sequence, but not the base sequence. An additional push of 1.5X got me bases. They are caps right under the position number line at the top of the window. Alternatively, push the "Bases" button to get directly there, with the center of the sequence shown. I like using the zoom buttons better since they give me a more intuitive sense of the scale of things, and how big the total sequence must be.
When doing the assignment is it normal to get a lower score from the BLAT comparing to the base pairs to the chicken genome than comparing them to the lancelet genome?
I don't know about "normal"--it just is what it is! I confess to being surprised myself. (Think about why this might be surprising!) One thing I learned poking around the "Homology" entry in Wikipedia last night (and no, I don't turn up my nose at Wikipedia) is that some level of matching between genes in different species is not "proof" that these genes descended from a common ancestor. In other words, the bigger score for the lancelet may be a coincidence. I just don't know. Of course, I'm just a teacher and not a scientist, but one of the cool things about this software is that we might just be doing REAL SCIENCE. It's a big universe in there, and NO ONE knows all the answers!
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