Lecture 4 Bioinformatics Flashcards
Homology
Like one another
We will deal with sequence homology, especially proteins
Bioinformatics
Exploded over last ten years
Sequence information
2 classes of homologs
- Paralogs - within species
2. Orthologs - Similar functions in different species
Paralogs
Within species, similar to each other
Orthologs
Similar functions in different species
Protein domains
Many proteins have single domains, some have lots.
Ex. Titan, 300+ domains
Hemoglobin VS. Myoglobin
Function is binding and transporting O2
VS. Reversible binding for O2, no transport in myoglobin
Compare the two sequences.
Sliding and Shuffling
2 Types of Sequence Alignment
- Sliding Alignment - slide along and see where they match
- Shuffling - take sequence and shuffle them
* Blosum 62 Substitution Matrix
Sliding Alignment
Slide sequences along each other and see where they match.
Ex. NCBI has Blast program that does this
Gives a simple score, can be 0-10
Shuffling Alignment
Take sequence and shuffle them (need high powered computer to do this)
Blosum 62 Substitution Matrix (25 varieties)
Gives scoring mechanism to look at chances for mutations
Scoring of conservative and nonconservative substitutions
Blosum 62
Substitution Matrix (shuffling alignment)
Scoring mechanism to look at changes for mutations
Minus score - the more negative, the more unlikely they are to occur
Ex. cysteine and tryptophan NOT favorable
Can distinguish between conservative and nonconservative
Substitution Matrix
Ex. Blosum 62
Branch chain AA are generally
interchangeable
Negative score on Blosum 62
Nonconservative
The more negative, the more unlikely to occur
Two AA that almost never mutate
Cysteine and Tryptophan (W)
Positive score on Blosum 62
Conservative substitution
Likely to occur
Hypervariable
5 that you compare, none are the same, tells you region of protein is not important for sturcture or function
If conserved over species
you know area is imp for structure/function of protein
Conservative substitution
Receives a positive score
Ex. Lysine for arginine
Nonconservative substitution
Is scored negatively
Ex. Lysine for tryptophan
BLAST
program by ncbi
Compares two sequences using sliding anaylsis
Letter in middle of two sequences
Same
+ sign in middle of two sequences
Positive, highly conserved
Frequent substitution
Space in middle of two sequences
Not conserved
