Module 2: Lesson 1 Flashcards
What is evolution?
Change in the heritable characteristics of biological populations over successive generations
Genome functions come from what?
Evolution
What is homology?
Similarity due to descent from a common ancestor
Are similarity and homology the same thing?
No.
What are the types of homology?
Orthologs and paralogs
What are orthologs?
Homologous sequences in different species that arose from a common ancestral gene during speciation; may or may not be responsible for a similar function.
What are paralogs?
Homologous sequences within a single species that arose from gene duplication.
What is pairwise alignment?
The process of lining up two sequences to achieve maximal levels of identity (and conservation) for the purpose of assessing the degree of similarity and the possibility of homology.
What are methods of aligning sequences?
By hand, dot plot, rigorous mathematical approach, and heuristic methods.
What is sequence identity?
The extent to which two nucleotide or amino acid sequences are invariant.
What do scoring matrices reflect in protein scoring systems?
Number of mutations to convert one protein to another, chemical similarity, and the probability of occurrence of each amino acid.
What are PAM limitations?
It is based on only one dataset, examines proteins with few differences, and is based mainly on small globular proteins so the matrix is biased.
What are the steps of dynamic programming?
Creation of alignment path matrix, stepwise calculation of score values, and backtracking (evaluation of the optimal path)
What are global alignment algorithms?
Algorithms that start at the beginning of two sequences and add gaps to each until the end of one is reached.
What are local alignment algorithms?
Algorithms that find the region(s) of highest similarity between two sequences and build the alignment outward from there.
