Determination of scores for substitutions and gaps

What is transition?

Insertion of a wrong nucleotide of the same type (purine instead of purine, pyrimidine instead of purimidine)

What is transversion?

Insertion of a wrong nucleotide of a different type (purine instead of pyrimidine or vice versa)

What does the letter q stand for?

Frequency of a single nucleotide in the sequence

What does the letter s stand for?

The assigned score to the substitution or a gap

What are PAM (Dayhoff) matrices?

Matrices used for scoring substitutions in protein sequences based on observed evolutionary changes

What is abbreviated under PAM?

Point Accepted Mutation

What is one PAM equal to?

Time for 1 substitution per 100 amino acids

What are BLOSUM matrices?

Matrices used for scoring substitutions in protein sequences, based on conserved regions of distantly related proteins at different levels of similarity

Which scores for PAM and BLOSUM would closely related sequences have?

Lower scores for PAM and higher scores for BLOSUM

Which scores for PAM and BLOSUM would NOT related sequences have?

Higher scores for PAM and lower scores for BLOSUM

What does the function g(k) stand for?

Penalty for introducing the gap of length k

What does the term subadditive mean?

A property of a function where the value of the function for the sum of two inputs is less than or equal to the sum of the function values for each input individually

What is the affine gap cost?

The most reasonable approximation to realistic costs of introducing gaps in sequence alignment, which accounts for both opening and extension penalties

Why is the Smith-Waterman-Beyer algorithm is not a good option for calculating the alignment, considering the gaps?

Because it has high computational complexity, which makes it inefficient for large sequences, particularly when numerous gaps may occur

What is the Gotoh’s algorithm?

A refined algorithm that improves upon the Smith-Waterman algorithm by efficiently handling affine gap penalties in sequence alignment

What is the computational effort in the Gotoh’s algorithm?

It’s roughly the same as in the Needleman-Wunsch algorithm with O(n*m), where n and m are rows and columns of the scoring matrix for sequences of lengths n and m, respectively

How many tables are used in the Gotoh’s algorithm?

3 tables are utilized: one for scores, one for gaps in the rows, and one for gaps in the columns

What is the joint probability?

It is the probability of two events occurring simultaneously

What is the conditional probability?

It is the probability of an event occurring given that another event has already occurred

What is the Bayes’ theorem?

Mathematical formula that describes the probability of an event based on prior knowledge of conditions related to the event. It calculates the likelihood of occurrence of an event given new evidence

Why do we use the logarithmic odds score?

It is used to express probabilities in a way that simplifies calculations by converting them into a linear scale