Calculate A Blosum Score for Each Position in A Sequence

The BLAST substitution matrix (BLoSUM) is a tool used in bioinformatics to measure the similarity between amino acids in protein sequences. This calculator helps you compute BLoSUM scores for each position in a sequence, providing valuable insights into sequence conservation and evolutionary relationships.

What is BLoSUM?

BLoSUM (Blocks of Amino Acid Substitution Matrices) is a family of substitution matrices used in sequence alignment algorithms like BLAST. These matrices contain log-odds scores that represent the probability of amino acid substitutions occurring in nature.

The BLoSUM matrices are constructed by analyzing multiple sequence alignments of proteins. The higher the BLoSUM score between two amino acids, the more likely they are to have evolved from a common ancestor.

BLoSUM scores are typically used in protein sequence analysis to identify conserved regions, functional domains, and evolutionary relationships between proteins.

How to Calculate BLoSUM Scores

Calculating BLoSUM scores involves comparing each amino acid in a protein sequence to every other amino acid using the BLoSUM matrix. The process is as follows:

Select a BLoSUM matrix (e.g., BLoSUM62, BLoSUM80)
Input your protein sequence
For each position in the sequence, compare the amino acid to all other amino acids in the matrix
Record the highest score for each position

BLoSUM Score Formula:

For a given amino acid pair (i, j):

Score(i,j) = log₂ (P(i,j)/P(i)P(j))

Where:

P(i,j) = observed frequency of amino acid pair (i,j)
P(i) = observed frequency of amino acid i
P(j) = observed frequency of amino acid j

The resulting scores are used to identify conserved regions in protein sequences, which are often functionally important.

Example Calculation

Let's calculate BLoSUM scores for the sequence "MKT" using the BLoSUM62 matrix.

Position	Amino Acid	Highest BLoSUM Score	Most Similar Amino Acid
1	M (Methionine)	5.7	L (Leucine)
2	K (Lysine)	4.1	R (Arginine)
3	T (Threonine)	3.4	S (Serine)

This example shows that Methionine is most similar to Leucine, Lysine to Arginine, and Threonine to Serine in the BLoSUM62 matrix.

Interpreting Results

Interpreting BLoSUM scores involves understanding the biological significance of the scores:

High scores (positive values): Indicate strong evolutionary conservation between amino acids
Low scores (negative values): Suggest amino acids that are less likely to substitute for each other
Zero scores: Represent amino acids that are statistically independent

Conserved regions (high scores) are often functionally important, while variable regions (low scores) may indicate flexibility in protein function.

BLoSUM scores should be used in conjunction with other bioinformatics tools for comprehensive sequence analysis.

FAQ

What is the difference between BLoSUM and PAM matrices?: BLoSUM matrices are based on observed amino acid substitutions in real protein sequences, while PAM matrices are based on point accepted mutations, which are hypothetical substitutions.
Which BLoSUM matrix should I use?: The choice depends on your specific analysis. Lower-numbered matrices (e.g., BLoSUM45) are better for closely related sequences, while higher-numbered matrices (e.g., BLoSUM90) work better for more divergent sequences.
Can BLoSUM scores be negative?: Yes, negative scores indicate amino acids that are less likely to substitute for each other based on the observed frequencies in the training set.
How do I visualize BLoSUM scores?: You can create a heatmap or use the calculator's built-in chart to visualize the scores for each position in your sequence.
Where can I find the original BLoSUM matrices?: The original BLoSUM matrices were published in the paper "Blocks of Amino Acid Substitution for Proteins" by Henikoff and Henikoff (1992).