Bioinformatics Flashcards
What is sequence alignment?
The process of lining up two or more sequences to achieve maximal levels of identity
Why do we align sequences?
- Assess the degree of similarity
- Assess possibility of homology
How do we computationally find the best alignment?
Dynamic programming
What is edit distance?
A way of quantifying how dissimilar two strings are to one another
How do we calculate edit distance?
Count the minimum number of edit operations required to transform one into the other
What are the different edit operations?
Substitution
Deletion
Insertion
What are some benefits of the LCS algorithm for pairwise alignment?
DNA Strings of equal length are not necessary
Finds longest subsequence common to all sequences
Insertion, deletion allowed
Time and space complexity is O(m * n)
What does a substitution matrix describe?
The rate at which one character in a sequence changes to others
What do global alignment algorithms do?
Start at the beginning of two sequences and add gaps until the end of either is reached
