Bioinfotmatics

Question 1

Transcriptome

Answer 1

The full range of coding RNA and non-coding RNA transcripts expressed by an organism

Question 2

Differential gene expression

Answer 2

Quantitative differences in gene expression levels between two samples that differ by one or more factors

Question 3

Sequencing read

Answer 3

The data string of A T C G bases corresponding to the sample DNA

Question 4

Alternative splicing

Answer 4

A regulated process during gene expression that results in a single gene coding for multiple transcripts or isoforms, and thus proteins

Question 5

Core principles of ribosome profiling

Answer 5

1. A translating ribosome strongly protects about 30 nucleotides or an mRNA from nuclease activity
2. Measuring the density of protected fragments on a given transcript provides a proxy for the rate of protein synthesis
3. Determining the positions of the protected fragments makes it possible to empirically measure the identity of translation products (I.e. where it start and end, ORFs, etc)

Question 6

Steps of ribosome sequencing

Answer 6

1. Collection of physiological sample
2. Inhibition of translation
3. Nuclease digestion to produce RPFs
4. Isolation of ribosomes
5. Isolation of RPFs
6. Next generation sequencing
7. Map fragments to the reference genome

Question 7

How to isolate ORFs

Answer 7

Canonical ORF identification:
1. ORFs are normally covered by high ribosomal footprints, and it’s density begins sharply at start codon, ends sharply at stop codon
2. Shows evidence of codon periodicity
3. Normally no coverage before the start codon or after the stop codon