bioinformatics lecture 5 (kinda important)

Why do we compare biological sequences? 🧬

Because similar sequences have similar structure and function,

letting us predict what genes do and how mutations affect them 🧠

What is the difference between similarity and homology? ⚠️

Similarity is a measured sequence match, while homology is an inferred evolutionary relationship (you never “measure” homology directly).

What is genome annotation? 🧩

The process of finding genes,

regulatory regions,

and functional elements in raw DNA sequence

to giving them biological meaning.

Why is gene finding easier in prokaryotes than eukaryotes? 🦠➡️🧬

Prokaryotes have dense genes and no introns,

while eukaryotes have introns, large gaps, and complex gene structures.

What makes gene prediction difficult in eukaryotic genomes? 🚧

Introns interrupt genes,

genes are spread far apart,

and exon lengths don’t always match reading frames.

What are the four main approaches used to find genes? 🔍

ORF detection,

pattern matching,

codon usage bias,

and homology searching (used together, not alone).

What is an ORF (Open Reading Frame)? 📖

A stretch of DNA that starts with ATG,

ends with a stop codon,

How does ORF detection work? 🔁

DNA is translated in all six reading frames

and long uninterrupted ORFs are searched for.

Why are long ORFs more likely to be real genes? 📏

Long ORFs are unlikely to occur by chance,

making them good gene candidates.

Why does ORF detection work best in prokaryotes and cDNA? ✅

Because they don’t contain introns that break up coding regions.

What is a major limitation of ORF detection? ❌

It performs poorly on eukaryotic genomic DNA

because introns disrupt reading frames.

What is pattern matching used for in gene finding? 🧠

To locate signals like promoters,

start sites,

splice sites,

and polyadenylation signals.

What is the Shine–Dalgarno sequence and where is it found? 🦠

A ribosome binding site in prokaryotes with consensus AGGAGG.

What is the Kozak sequence and where is it found? 🧬

A eukaryotic translation start signal with consensus gccRccAUGG.

What does the polyadenylation signal do? ✂️

It marks the 3′ end of a gene and signals where the poly-A tail is added (AAUAAA).

Why does pattern matching not give complete gene models? ⚠️

It only identifies approximate locations, not full exon–intron structures.

What is codon usage bias? 🔄

Organisms prefer certain codons over others to code for the same amino acid.

Why does codon usage bias exist? ⚙️

Because some codons match abundant tRNAs and are translated faster and more efficiently.

Why is codon bias strongest in highly expressed genes? 🚀

These genes benefit most from fast and efficient translation.

Why is codon usage bias only supporting evidence for a gene? ⚠️

It suggests coding potential but cannot prove a gene exists on its own.

What is homology searching? 🔗

Comparing a sequence to known sequences in databases to find similar genes or proteins.

Why is homology searching powerful? 💪

It can identify known genes, protein families, and functional domains.

What is a limitation of homology searching? 🚫

It can only find genes that are already represented in databases.

Why are protein alignments often better than DNA for homology searches? 🧠

Proteins are more conserved over evolution and better reflect function.

What is a reference genome? 🗺️

A standard genome used as a framework to compare and interpret new sequencing data.

What is re-sequencing? 🔄

Aligning new sequencing reads to a reference genome instead of assembling from scratch.

What do differences between a sample and the reference genome represent? 🧬

Genetic variants such as SNPs, insertions, or deletions.

Why do almost all diseases have a genetic component? 🧠

Genes influence how the body develops and responds, even when environment also plays a role.

What is a monogenic (Mendelian) disease? 🧬

A disease caused by a mutation in a single gene.

What is a complex (multifactorial) disease? 🌍

A disease caused by many genes plus environmental factors.

What is linkage analysis? 🧬➡️🧬

A family-based method that finds disease genes by tracking linked genetic markers.

Why does linkage analysis work well for rare Mendelian diseases? 👨‍👩‍👧‍👦

Because the disease follows clear inheritance patterns in families.

What is a limitation of linkage analysis? ⚠️

It has low resolution and identifies large genomic regions.

What is GWAS (Genome-Wide Association Study)? 🌐

A population-based method that links SNPs to disease traits.

Why is GWAS good for complex diseases? 🧠

It can detect small genetic effects across many individuals.

What is a major limitation of GWAS? ⚠️

It is prone to false positives and does not prove causation.

What is the key difference between linkage analysis and GWAS? 🔍

Linkage uses families and finds rare disease genes, while GWAS uses populations to study complex diseases.

Why has exome sequencing transformed rare disease genetics? ⚡

It sequences all genes at once, allowing rapid identification of disease-causing mutations.

Why is functional validation still needed after sequencing? 🧪

Because finding a mutation does not automatically prove it causes disease.