DNA Sequence Analysis Toolkit

This toolkit provides a series of functions for analyzing DNA sequences to identify codon patterns, open reading frames (ORFs), and the longest ORF within a sequence.

Overview

The project is divided into the following steps:

1. Finding all start codons: Locate all occurrences of the ATG start codon.
2. Finding in-register stop codons: Identify the first stop codon (TGA, TAG, or TAA) in-frame.
3. Identifying all ORFs: Determine the ranges of all open reading frames in the sequence.
4. Finding the longest ORF: Extract the longest open reading frame from the sequence.

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Steps and Implementation Details

Step 1: Implementing the find_all_starts Function

This function scans a DNA sequence and identifies all starting positions of the ATG codon.

Step 2: Implementing the find_first_in_register_stop Function

You will write a function called find_first_in_register_stop that scans a DNA sequence and identifies the first occurrence of a stop codon (TGA, TAG, or TAA) in the register (every 3 nucleotides). If the stop codon is not found, the function will return -1.

Step 3: Implementing the all_orfs_range Function

You will implement a function called all_orfs_range that scans a DNA sequence and identifies all open reading frames (ORFs) by finding the start codons (ATG) and the corresponding stop codons (TGA, TAG, TAA), and returns the range of each ORF.

Step 4: Implementing the longest_orf Function

You will implement a function called longest_orf that scans a DNA sequence, finds all open reading frames (ORFs), and returns the longest ORF from the sequence.