Lecture 09 - Bioinformatics Flashcards
What is substitution
a sequence change where compared to a reference sequence, one nucleotide is replaced by another
What is transition
the change from one purine to another purine (A>G) or pyrimidine to another pyrimidine (C>T)
What is transversion
the change from a purine to a pyrimidine or the change from a pyrimidine to a purine
What are insertions
a sequence change where compared to the reference sequence one or more nucleotides are inserted and where the insertion is not a copy of a sequence immediately 5’
What is duplication
sequence change where, compared to the reference sequence a copy of one or more nucleotides are inserted directly 3’ of the original copy of that sequence
What are deletions
a sequence change where, compared to a reference sequence one or more nucleotides are not present
What is identity
the extent to which two sequences have the same residues at the same positions in an alignment (often expressed as a percentage)
What is similarity
the extent to which nucleotide and protein sequences are related (expressed as percent sequence identity and or percent positive substitutions)
What is pairwise alignment
the alignment of two sequences
What is multiple alignment
alignment of three or more sequences
What is alignment
the process or result of matching up the sequence to achieve maximal levels of the same residues at the same positions in an alignment
What is global alignment
aligning complete sequences
What is local alignment
identify only the most similar segments or sequences of patterns
What are the ways to create an alignment
by hand, dynamic programing, heuristic methods
What is BLAST
Basic local alignment search tool
