Scientific computing

(for the rest of us)


What is recursion, if not recursion persevering? In this module, we will see how to call functions recursively, and discuss when this is appropriate in real life.

A very important type of sequences in molecular biology are palyndromic sequences, where reading them on one strand gives a sequence that is complementary to the sequence we get when reading it on the other strand. For example, the EcoR1 restriction site has a sequence of GAATTC on the 5’ to 3' strand, and its complement is CTTAAG on the 3’ to 5’ strand.

Can we write a function to check whether a sequence is a palyndrome? Absolutely! And we will do so using recursion. But what is recursion? In a few words, it is the process of a function calling itself until some stopping condition has been met. For example, our function can check that the first basis on the 5’ to 3’ strand is the same as the last basis on the 3’ to 5' strand, and then do the second and second to last, until the sequence has been exhausted or a mismatch found.

Using recursion, we can write this function without using a loop!

function palyndrome(seq5, seq3, index = 1)
    if index > length(seq5)
        return true
    @info "Checking position $(index)"
    if seq5[index] == seq3[end - index + 1]
        return palyndrome(seq5, seq3, index + 1)
        return false
palyndrome (generic function with 2 methods)

First, let’s ensure that this function works:

palyndrome("GAATTC", "CTTAAG")
palyndrome("GATTTC", "CTAAAG")

Now, let’s take a little dive into what happens internally. We start by checking the stop condition (this is counter-intuitive, but it be like that sometimes). If we have met the stop conditions, i.e. if we have read the sequence across all sites, then we know it is a palyndrome and we return true.

The end-index+1 index in the comparison has a +1 because Julia indexes from 1, not 0, and this makes a lot of people angry, because programmers are actively looking for reasons to be angry sometimes. Just voice on opinion about the tabulations versus spaces, and you’ll see what we mean.

If we have not yet reached the end of the sequence, we perform the comparison. If the two bases are different, the sequence is not a palyndrome, and we return false; but if the two bases match, we call the function again, this time with the next index value.

As with while loops, recursion will stop whenever recursion will stop whenever recursion will stop whenev… sorry what we were going to say is: you need to ensure that the stop condition can be reached.

There are a few reasons to use recursion as opposed to loops. In some cases (like looking up inside folders, or looking up values in binary trees), this is a much more efficient way to work. Recursion can work with distributed computing as well, by starting different calls to the function on multiple threads or machines.

But this is not to say that recursion has not issues - it can perform worse than iteration in a substantial amount of cases, and is generally requiring that you think about problems in a different way. In any case, it is an important tool to have in your programming toolbox!