Sequence Alignments, Discussion, Spring 2008
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Please use this page to ask questions or post notes about the Sequence Alignments assignment.--Dr. Moss 09:58, 5 February 2008 (EST)
Was the due date for this assignment changed? i believe the last time i looked at the due date it said feb 15?--Christina 16:54, 6 February 2008 (EST)
Yes. I regret the mistake and apologize. As Dr. Byrne said, the assignments are due 10 days after the class in which they were assigned. I gave the lecture on sequence alignments last Wednesday, so assignment is due Friday of this week. I will give you some extra days to complete it, until Monday. But you have another assignment coming ... --Dr. Moss 17:02, 6 February 2008 (EST)
I am trying to do question 4 on the assignment and at iteration 2 i formatted the results to show the matrix PSSM but then when i hit view report a bunch of letters and numbers came up. can anyone send me in the right direction with the matrix part of the question?--Christina 16:49, 10 February 2008 (EST)
I find the same problem as Christina for problem 4 for the iteration 2! what are you looking for building matrix? please help!
I was simply asking which ones found new proteins, not anything about the matrix. Don't worry about this. --Dr. Moss 11:51, 13 February 2008 (EST)
For question 6a a) In the human sequence, what are roughly the positions of the identical sequences corresponding to the longest two lines? what are you asking for ?? because I compute both sequences and I am scrolling the sequence at the bottom and I dont know what I am counting? So unless I understand 6a then I can 6b. Please help.
For 6a, I'm simply asking for the numbers indicating the position of the human sequences matching the fly sequence, like "234-251". (You don't really need to get 6a to get 6b.)--Dr. Moss 21:21, 13 February 2008 (EST)
For question 5a finding the number of repeats... when i scroll down and to the right the repeats seem to be going on forever. i get one diagonal line that spans the entire box but then the rest of the diagonal lines go on forever. is there some other way to find the number of repeats that i'm missing. --Christina 21:04, 13 February 2008 (EST)
First try changing the zoom (1:1, 1:2, etc.) so you see the whole sequence at once. The repeats don't actually go on forever. Write again if you don't get it after changing the zoom. --Dr. Moss 21:21, 13 February 2008 (EST)
i changed the zoom and got it(i think). Now when i do question 6 in dotlet i don't get any long diagonal lines they are all short so i should find the longest one i can and place the cursor at the beginning and then again at the end of the line to get the position. is this correct?
Yes, that's correct. --Dr. Moss 22:13, 14 February 2008 (EST)
I am trying to do #9 and I am not able to open my results in BoxShade Server and what do you mean putting Plus "A" or "B" ? If you select four sequences for it then do you go in a row such as A, B, C, and D? Please help. If i am not able to solve 9, I can not do 10. For 7 Local alignment, I receive 3 results so what should I do? thank you.
Be sure you are pasting in the clustalW alignment, maybe select "aln" format. Take a look at the names of the sequences and shorten the names so that you know what species it comes from and whether it is Lin28A or Lin28B. To do #10, all you need is the clustalW alignment. Can you get that? For #7, give the results of each section of the local alignment. --Dr. Moss 16:00, 15 February 2008 (EST)
I have problem finishing the problem no. 3 (c) and (d). I got three answers for local alignment (question no. 7). With question no. 9, I am getting answer in a single line (around 40 amino acids). Also with question 8 I got answer (around 15 amino acids), please give some directions. T hank you. --nimish 16:51, 15 February 2008 (EST)
A) Read my replies to previous questions. B) You will have to be more specific with your questions. C) It's getting to be too late to ask questions about this assignment. --Dr. Moss 00:39, 16 February 2008 (EST)
