Bioformatics

Question 1

What is Sequence analysis?

Answer 1

A comparison of genes within a species or between different species to show relations between species or protein functions. Determined genes that encode proteins and RNA genes.

Question 2

Sangers sequence analysis

Answer 2

DNA Denaturation due to heat.

Question 3

What is next-gen sequencing?

Answer 3

It generates masses of DNA sequence data that’s richer and more complete than sanger. Makes large scale whole genome sequencing possible for researchers.

Question 4

Sequence Homology Software

Answer 4

BLAST. An algorithm which searches databases, to detect a specific query, then when it finds a match, it searches for shared nucleotides at the end of the seed to end the match.

Question 5

Different types of BLAST?

Answer 5

BLASTN
BLASTP
PSI BLAST
BLASTX
MegaBLAST

Question 6

BLASTN

Answer 6

Basic nucleotide sequence searches.

Question 7

BLASTP

Answer 7

Used to search Amino Acid sequences.

Question 8

PSI-BLAST

Answer 8

Analyses the relationships between divergently evolved proteins.

Question 9

BLASTX & BLASTN variants

Answer 9

Six frame translation for protein and nucleotides respectively in the search.

Question 10

MegaBLAST

Answer 10

BLASTs several sequences at once to cut down on processing and server reporting time.

Question 11

Genome annotation

Answer 11

The marking of genes and other biological features in DNA sequencing.

Question 12

Modelling evolutionary biology

Answer 12

Study of the origin and descents of species and there’s change over time.
Trace, compare, track.

Question 13

GWAS

Answer 13

Examination of many common genetic variants in different individuals to see if they identify with a trait.
SNPs and traits of major diseases.

Question 14

Gene expression analysis

Answer 14

Determines the gene implicated in a disorder. Comparison of cancerous and non cancerous cells to determine the transcripts (Up&Down Regulation).

Question 15

Heatmaps

Answer 15

Show how a particular variable influenced gene expression.

Question 16

Hierarchical clustering

Answer 16

Objects being more related to nearby objects than to those further away.

Question 17

Analysis of protein expression

Answer 17

Protein microarrays

HT MS to provide a snapshot of the protein present in a biological sample.

Question 18

Protein-Protein Interaction

Answer 18

Physical contact of two or more proteins as a result of a biological event or electrostatic forces. Enables creation of large protein interaction networks, empowers biochemical signalling and disease pathogenesis. Provides new therapeutic targets.

Question 19

Network analysis

Answer 19

Understands the relationship with biological networks such as protein-protein interaction networks.

Question 20

Network biology

Answer 20

Integrates many different data types which are connected either physically or functionally.

Question 21

Three types of databases

Answer 21

Data from empirical methods i.e. gene knockout.
Predicted data.
Both.

Question 22

Meta-database

Answer 22

Incorporates data compiled from multiple other databases.

Question 23

Key databases

Answer 23

Nuclei can acid sequence databases.
Protein databases.
Meta-databases.

Question 24

Nucleic acid sequence database

Answer 24

DNA sequence
Genomics
RNA sequence. 
GeneBank
EMBL
DDBJ.

Question 25

Protein database

Answer 25

``` Protein sequence Proteomics Ligands and drugs. SWISS PROT PIR MIPs TrEMBL. ```

Question 26

Meta- databases

Answer 26

Gene-set enrichment analysis | Functional annotation.

Question 27

What is Bioformatics?

Answer 27

The creation and advancement of databases, algorithms, computational and statistical techniques in order to solve formal and practical problems in biological data.