Effects:

May alter protein sequence or prevent correct protein formation.
Can cause genetic disorders and cancers, or create beneficial variation for evolution.
Many mutations are neutral or silent (no effect on protein).

Definition: Way of dividing DNA/RNA into consecutive, non-overlapping codons (triplets).
A change in reading frame changes the codons and thus the amino acid sequence.
Both strands (coding and complementary) are read 5' to 3'; each has 3 possible frames depending on the starting position (shift = 0, 1, 2).
6 total reading frames: 3 on each of 2 strands.

DNA $\to$ pre-mRNA (has introns/exons) $\to$ splicing $\to$ mature mRNA $\to$ translation.
Only mature mRNA is read by the ribosome.

Definition: Continuous stretch from a start codon to a stop codon, without internal stop codons.
The longer the ORF, the higher the chance it is protein-coding.
Objective: Find all ORFs, usually the longest one is functionally important.

For a given DNA strand (Forward):
- +0 frame: starts at base 0
- +1 frame: starts at base 1
- +2 frame: starts at base 2
For the reverse complement strand:
- –0, –1, –2 (as above, starting on bases 0, 1, 2 after reverse-complementing).
Frame examples (for S = ATGAAGTGACCTTAG):
- +0: ATG AAG TGA ...
- +1: TGA AGT GAC ...
- +2: GAA GTG ACC ...
- Compute reverse complement, then same +0, +1, +2 frames.

Read Input: DNA sequence $S$, length $n$; min ORF length $L_{min}$.
Strand Setup:
- Forward: $S$ as given.
- Reverse: reverse $S$, take complement (A $\leftrightarrow$ T, C $\leftrightarrow$ G).
Frame Setup:
- For each strand, make 3 frames (shifts 0, 1, 2).
ORF Search in Each Frame:
- Go codon-by-codon.
- When start codon (ATG) found, mark position.
- Continue in same frame until stop codon (TAA/TAG/TGA).
- Extract from start to stop (inclusive).
- If ORF length $\ge L_{min}$, record: strand, frame, start/end, length, sequence.
- Repeat for all starts/stops in all frames.
Result: List ORFs by position, frame, strand, sequence, length.

Complementary strand ORFs may or may not be functionally relevant.
If there are start and stop codons, but an intervening stop codon appears in-frame, it's not a valid ORF.
If a stop codon is present without a start codon, it is not an ORF.

$S$ = 5’-ATGAAGTGACCTTAG-3’