A repository of Python solutions to the code challenges from Unit 1 of Bioinformatics Algorithms (Stepik).
Before opening the code files, I recommend quickly reading about the biology background of this project to get a clearer sense of the purpose of each program/function.
The majority of the files in this repo are for a single function. Most of these small functions contribute to the larger Final DnaA Box Finder program.
The Salmonella enterica genome is included as test data. The final DnaA Box Finder identified the S. enterica DnaA box as TTATCCACA. An existing UniProt database entry confirms that the DnaA sequence is 5'-TTATC[CA]A[CA]A-3' - a successful match!
- Find the number of times a k-mer appears in the genome
- Find the most frequent k-mer in a genome given the k value
- Find the location of a specific k-mer in a genome
- Find frequent k-mers that cluster together into clumps in the genome
