Bioinformatics Flashcards
Substitution
Sequence change where one nucleotide is replaced by another nucleotide
Transition
Change from one purine to another purine (A>G) OR change rom one pyrimidine to another pyrimidine (C>T)
Transversion
Change from purine to pyrimidine (A>T), and vice verse (C>G)
Insertion
One or more nucleotides are inserted AND where the insertion is not a copy of a sequence immediately 5’
Duplication
Copy of one or more nucleotides are inserted directly 3’ of the original copy of that sequence
Deletions
One or more nucleotides are deleted
Identity
The extent (%) to which two (nucleotide or amino acid) sequences have the same residues at the same position in an alignment
Similarity
The extent (%) to which nucleotide sequences are related
NOTE: expressed as %sequence identity and/ or %positive substitutions
Differentiate homologs vs paralogs
Homolog: genes inherited from a common ancestor between 2 different species
Paralog: duplicate genes within the same species
Alignment
Aligning nucleotide/ amino acid residues of two or more sequences so that differences can be identified
Pairwise vs Multiple alignment
Pairwise: alignment of two sequences
Multiple: alignmnet of 3 or more sequences
Differentiate Global vs Local alignment types
Global: align complete sequences
Local: identify only most similar segments/ sequence patterns/ motifs
Differentiate Dynamic Programming vs BLAST
Dynamic programming:
- more precise but requires large computer load
- global and local alignmnet
BLAST:
- “basic local alignment search tool”
- a heuristic method; takes shortcuts to get an approximation
- local alignmnet
“The __ the E-value, the less likely a match is due to chance”
- “The smaller the E-value, the less likely a match is due to chance”
- longer sequences will have higher E-values
Mnemonic: Purines
“Pure silver;” Pur = AG
