Comparison of DNA Sequences with Dynamic Programming and Scoring Scheme

Study Notes

Sequence Alignment

Global alignment of DNA sequences using dynamic programming and a scoring scheme is possible.
Scoring scheme:
- Match: +3
- Mismatch: -2
- Gap: -3

Practice Questions

Align DNA sequences using dynamic programming and the provided scoring scheme.
Examples:
- Seq 1: GCTTAGC
- Seq 2: GCATTGC

Gap Penalty

Gap penalty score: g(g) = -d - (g -1) e
Linear gap penalty score: d = gap opening penalty, e = gap extension penalty, g = gap length
Affine gap penalty score: g(g) = -d - (g -1) e

Scoring Insertions or Deletions

Using GAP penalty, score insertions or deletions.
Example:
- Total Score: 4
- Total Score: 8 + (-3.2) = 4.8

Substitution Matrices

Used to score substitution events in alignments.
Particularly important in protein sequence alignments.
Each scoring matrix represents a particular theory of evolution.
Examples of substitution matrices:
- Identity scoring matrix
- Genetic code scoring scheme
- Chemical Similarity Scoring
- PAM substitution matrices

Identity Scoring Matrix

Simplest scoring scheme.
Score 1 for identical pairs.
Score 0 for non-identical pairs.
Unable to detect similarity.

Genetic Code Scoring Scheme

Introduced by Fitch in 1966.
Scores based on the number of nucleotide base changes required to interconvert the codons for the two amino acids.
Used in the construction of phylogenetic trees and in the determination of homology between protein sequences.

Chemical Similarity Scoring

Introduced by MacLachlan in 1972.
Gives greater weight to the alignment of amino acids with similar physico-chemical properties.
Amino acids are classified based on polar or non-polar character, size, shape, and charge.

PAM Substitution Matrices

Constructed by Dayhoff, Schwarz, and Orcutt in 1978.
Based on 71 protein families with 85% identical sequences.
Obtained frequencies for residue X being substituted by residue Y over time period Z.
Ignores evolutionary direction.
Based on 1572 residue changes.
Defined a substitution matrix as 1 PAM (point accepted mutation) if the expected number of substitutions was 1% of the sequence length.

Description

Explore the practice questions on globally aligning DNA sequences using dynamic programming and a specific scoring scheme. Test your knowledge on sequence alignment with provided sequences, GCTTAGC and GCATTGC, along with scoring criteria for matches, mismatches, and gaps.