Regarding homework questions for the splicing graph

[Marcel Schulz]

Hello,

as there have been a couple of questions regarding question 2 in homework 5. I have compiled them and give the answers below.

Concerning Question 2.1.
Q: The question concerns on what the implications of showing the "reverse strand" is.  In the lecture, the forward coding strand was used I believe.  So are we supposed to convert the "reverse" strand into the coding strand?
A: No you are not supposed to reverse the sequence although it is a valid thought and in the end a matter of defintion. But because the splicing graph is a directed graph it should change the direction of edges here.

Q:Also, do we need to draw the splicing graph based on the sequence given on the reverse strand, or we have to convert it to sequence on forward strand?
A:Please use the sequence from the forward strand but draw the edges in reverse direction. 

Concerning Question 2.2.

Q:I don't understand this question because the instructions are too short

and not explanatory enough. What are we asked here? Are we just supposed
to list the positions at which they differ? Are we just supposed to say
'this is spliced this way, the other is not'?

Please provide a more clear explanation.

A:As discussed in the lecture the splicing graph can be used to deduce possible alternative splicing events. A common method to do that is to compare two transcripts by their paths as defined in the splicing graph. You are supposed to name the splicing events as identified by comparing the paths in the graph for S_1 versus S_2, S_1 versus S_3, etc, but dont need to give the sequence position. For 2a,2b,and 2c, please, list the alternative splicing event for each S_i in the comparison. You should notice something when you do that, and explain your observation shortly in 2d.

If you find it hard to come up with the Alternative splicing events from the graph you may find it useful to look at the attached Figure AS_events_in_splicing_graphs.jpg, Figure 1 in the following paper:

Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse

http://www.biomedcentral.com/1471-2164/10/S1/S5

Note that in this paper

what is defined as competing 5'/ 3' splice sites in the lecture slide is referred to as alternative donor / acceptor site.

The term alternative donor/acceptor site is also common in the literature.

You may use either one of the terms from the lecture or the paper in your answer.

Hope that helps,

Marcel