Bioinformatics Lecture 3 Flashcards
synonymous mutation
same amino acid
non-synonymous mutation
missense and nonsense mutations
missense mutation
different amino acid
lead to different amino acid
nonsense mutation
replaced by stop codon
often produces non-functioning protein
homology
a sequence or species shares the same ancestor
MSA
multiple sequence alignment
shows conserved and less conserved regions
conserved proteins are likely to be functional
Protein sequence alignment
how closely are proteins related
how homologous
alignment scoring
matches and mismatches with substitution matrix
in the end gap penalty is subtracted
global pairwise sequence alignment
an algorithm
takes substitution matrix
traces back steps
gives perfect alignmnet
three possible roads
high
low
middle road
algorithmic complexity
how many steps you need
Needleman Wunsch
global pair wise alignment
comparing two whole sequences
Smith Waterman
local pair wise alignment
comparing only some parts
theory driven
gap at sequence ends are not punished
Henikoff and Henikoff
1992 first BLOSUM score takes amino acid frequency into account positive: preferred substitution negative: avoided substitution zero: random
BLOSUM n
always integer
made from n% sequence alignment
in practice: most often 62%
