Bioinformatics is the science of storing, retrieving, and analyzing large amounts of biological information. It's a discipline that combines biology, computer science, information engineering, mathematics, and statistics to analyze and interpret biological data. One of the critical areas of bioinformatics is DNA sequence analysis.
In this project, we deal with a real-life bioinformatics problem: analyzing DNA sequences in multi-FASTA format. A FASTA file is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes.
Analyzing and understanding DNA sequences is a fundamental task in bioinformatics. It's through this analysis that we can understand the genetic makeup of organisms, identify genetic diseases, develop drugs, perform forensics analysis, and even understand and trace the evolution of species.
The DNA sequence analysis helps answer various important questions such as:
- How many records (sequences) are in the file?
- What are the lengths of the sequences in the file? Which sequence is the longest and which one is the shortest?
- How can we identify open reading frames (ORFs) in each sequence?
- Can we identify all repeats of a certain length in all sequences in the file?
Answering these questions allows us to better understand the structure and function of genomes, and can provide insights into the evolutionary processes that shape the DNA.
This project revolves around the development of a Python program to answer the above questions. You will need to read a file containing DNA sequences in multi-FASTA format and compute the answers.
A record in a FASTA file is defined as a single-line header, followed by lines of sequence data. The header line is distinguished from the sequence data by a greater-than (">") symbol in the first column. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is an optional description of the entry. There should be no space between the ">" and the first letter of the identifier.
You will use an example file (dna.example.fasta) to test your work during the development of the program(s). You will be given a different input file to launch the exam itself.
The quiz itself contains the specific multiple-choice questions you need to answer for the file you will be provided.
For the full problem statement, please refer to the problem file.
You can start by understanding the problem in detail, and then attempt to solve it yourself. After you've finished (or if you're stuck), you can check the solution. The solution will be explained in detail to aid your understanding.
Remember, this is a practical, real-life problem. Take your time and enjoy the challenge!