Bioinformatics Flashcards
0
Q
Aspects of sequence analysis
A
- gene and promoter prediction
- RNA secondary structure and gene expression
- protein sequence analysis
- restriction mapping for cloning and primer design for PCR
1
Q
Purposes of DNA sequencing in bioinformatics
A
- able to convert between sequence formats
- percentage nucleotide composition
- restriction analysis (looking for restriction sites)
- primer design
- finding coding and non-coding features
- removal of vector sequence
- gene prediction
- getting the final protein
2
Q
Aspects of bioinformatics and cloning
A
- retrieving the sequence of interest
- identifying restriction enzyme sites
- engineering new sites using PCR
- sequencing an insert
3
Q
What is an SNP?
A
- a DNA sequence variation occurring commonly within a population in which a single nucleotide in the genome differs between members of a species
4
Q
What does fst measure?
A
The similarity between populations due to genetic structure
5
Q
Implications of genetic diversity
A
- could affect gene expression if in a TF site
- could affect splicing
- could affect protein abundance or function
- potential disease phenotype
6
Q
Uses of a functional interaction network
A
- function prediction
- network analysis for important proteins
7
Q
Applications of network/systems biology
A
- finding important genes
- viewing connections between genes and the effect of knocking one out
- overlaying high-throughput data
- GWAS analysis
- integrating data from different sources
- multi-disciplinary research
8
Q
Types of signatures for functional regions
A
- position weight matrix
- protein signatures
- pattern
- matrix/profile
- hidden markov model
9
Q
Features of a genomic context
A
- which strand it is encoded on
- Exon/intron structure
- promoter region
- other features
- genes up and downstream
10
Q
Models of evolution
A
- nucleotide substitution
- amino acid substitution
- demographic
- molecular clock
- phyllo geographic
11
Q
What does GWAS stand for?
A
Genome wide association studies
12
Q
Workflow of experiment for a pharmacogenetic gene
A
- GWAS studies and data king to identify candidate genes
- functional analysis and validation of candidate gens
- drug id and population studies
- point of care and personalized medicine
13
Q
Properties to assess in a systems nework
A
- hubs
- degree
- betweenness
- closeness
14
Q
What is a gene signature?
A
A group of genes whose combined expression pattern is uniquely characteristic of a biological phenotype
