Identify aberrant splicing in DNA sequence

Question

[Ana]

Hi all,

I'm really new in this stuff of bioinformatics and I'm having some trouble to understand how to do some things. Right now I have a DNA sequence that has already been aligned and everything. As far as I understood it has been used TopHat to do so, so it came with the other output files that this tool generates.

At this point, I have some questions that I want to answer by analysing the sequence:

• Identify aberrant alternative splicing;
• Identify mitochondrial genes.

How can I do that? I don't even know really how to start. Someone can give me some tips please?

Best regards,
Ana

Answer 1

[Devon Ryan]

For finding differences in splicing (determining whether they're actually aberrant is vastly more complicated and will likely require further experiments) one would typically start with tools like cufflinks or stringTie. I should note that I'm assuming that you're looking for presumably novel splicing events, given the usage of "aberrant" in your question. In general, the search term you're looking for is "differential splicing".

For mitochondrial genes, presumably you mapped against the mitochondrial genome. Mitochondrial DNA is essentially just end to end genes packed together, so I'm not sure there's much in the way of new genes to find there.

[Ana]

Thanks for the help! Yes, what I'm thinking about is when an event of alternative splicing happens but then it generates some kind of mutation. So what you are saying is that I should search for differential splicing, is that it? Can you explain me or give me some links of what it consists on?

About the second question, in first place I must say that it was some biology experts that asked me about this, so I'm also trying to, somehow, get their point of view. Given this, is there way for, given a tophat output I can determine, for example the sequences that will have a place in mitochondrial genes?

Ps: I'm student in informatics engineer and there are some concepts of biology that often are hard for me understand at first.