5 Genomics and Genome Analysis Free Online FlashCards

What is a genome?

A genome is an organism’s complete set of genetic material. Most organisms use DNA, while some viruses use RNA.

How do exons and introns differ?

Exons remain in mature RNA, while introns are generally removed during RNA processing.

What is a genome assembly?

A genome assembly computationally combines overlapping sequencing reads to reconstruct longer sequences. It is a data-based representation, not the genome itself.

How does a scaffold differ from a contig?

A contig is a continuous assembled sequence with no gaps. A scaffold orders and orients contigs and may include estimated gaps.

Why can long reads help assemble repetitive regions?

Long reads can span many repeats and help connect distant genomic regions, making them useful where short reads are difficult to place.

What does assembly N50 measure?

N50 is the length at which sequences of that length or longer account for half of the total assembly length when sequences are ordered from longest to shortest.

What does a high N50 not prove?

A higher N50 can indicate greater continuity, but it does not by itself establish that an assembly is correct or complete.

Why report an assembly accession and version?

Record the organism and exact assembly accession and version. Coordinates and annotations are tied to an assembly version and may not match directly across versions.

What does structural annotation identify?

Structural annotation locates genomic features and defines their boundaries, such as genes, transcripts, exons, coding sequences, and noncoding RNA genes.

What does functional annotation assign?

Functional annotation assigns likely roles to genomic features, such as a protein’s function, a gene’s pathway, or a sequence’s regulatory activity.

What can RNA evidence and protein similarity support in annotation?

RNA evidence can support an expressed transcript, while protein similarity can help identify a coding region or infer a likely function.

Why are genome annotations not guarantees of function?

Annotations are evidence-based predictions and interpretations, not guarantees of biological function. Limited evidence or an incomplete assembly can lead to missing or incorrectly modeled features.