I've just started a grad fellowship at NESCent.  My main goal for my time here is to produce papers that utilize data from the tree of sex data that I have been helping to collect.  However, I do have a few ancillary goals for my time here one of which is to become a better programmer.  I've asked a few people (way smarter than me) over the last couple of years how to become really good in a particular language.  The most frequent response that I have received is to just do "something" each and every day in whatever language it is that you are working on.  To that end I am supplementing my normal programming with the challenges at Rosalind.  This is a great website that has all kinds of programming challenges that you can attempt to solve.  The site seems to have a python focus, buts lots of members solve problems with every language you can think of.  I’ve decided that I am going to start at the beginning of the bioinformatics challenges and try and solve about a problem a day in R and in Python.  The first ones are really simple so I did three in R today.

Challenge 1: A string is simply an ordered collection of symbols selected from some alphabet and formed into a word; the length of a string is the number of symbols that it contains.  An example of a length 21 DNA string (whose alphabet contains the symbols 'A', 'C', 'G', and 'T') is "ATGCTTCAGAAAGGTCTTACG."

Given: A DNA string s of length at most 1000 nt.

Return: Four integers (separated by spaces) counting the respective number of times that the symbols 'A', 'C', 'G', and 'T' occur in s.

Challenge 2: An RNA string is a string formed from the alphabet containing 'A', 'C', 'G', and 'U'. Given a DNA string t corresponding to a coding strand, its transcribed RNA string u is formed by replacing all occurrences of 'T' in t with 'U' in u.

Given: A DNA string t having length at most 1000 nt.

Return: The transcribed RNA string of t.

Challenge 3: In DNA strings, symbols 'A' and 'T' are complements of each other, as are 'C' and 'G'.  The reverse complement of a DNA string s is the string sc formed by reversing the symbols of s, then taking the complement of each symbol (e.g., the reverse complement of "GTCA" is "TGAC").

Given: A DNA string s of length at most 1000 bp.

Return: The reverse complement sc of s.

cheers from NESCent