MOLGEN_MOD2.1_Understanding Genomes and Sequencing Technologies

These flashcards cover key vocabulary terms and concepts related to genomes, sequencing technologies, and assembly methods, as discussed in the lecture.

Genome

The complete DNA or RNA sequence of an organism that encodes all genetic instructions for growth, function, and reproduction.

Genes

Functional units of heredity that are arranged linearly on chromosomes.

Chromosomes

Structures that organize and carry genes in the genome, akin to chapters in a book.

Genotype

The genetic makeup of an organism.

Phenotype

The observable traits or characteristics of an organism.

Mutations

Changes in the genomic sequence that introduce variation and drive evolution.

Sequencing

The process of determining the order of nucleotides in DNA or RNA.

Base pairs (bp)

Units of measurement in DNA sequencing, with the human genome containing approximately 3.2 billion bp.

Overlapping reads

Simultaneously read fragments of DNA that are aligned to reconstruct the original sequence.

Assembly software

Computer programs used to align overlapping reads for genome reconstruction.

Short overlaps

Common overlaps (like 6 bp) that are too frequent for uniqueness in genome assembly.

Long overlaps

More reliable overlaps (15-16 bp) that improve confidence in genome assembly.

Bioinformatics

The field that combines biology and computer science to analyze and interpret genomic data.

Genomic maps

Reference frameworks that position genetic landmarks within the genome for assembly and verification.

Landmarks

Notable genetic features such as genes and SNPs used for genomic mapping.

Contigs

Overlapping DNA fragments that are assembled to represent the entire genome.

Clone-contig sequencing

A map-first sequencing method that uses organized clones guided by a genomic map.

Shotgun sequencing

A sequence-first method that randomly fragments DNA for assembly using algorithms.

Hybrid approaches

Methods that combine both clone-contig and shotgun sequencing for greater efficiency and accuracy.

Tandem repeats

Short motifs that are repeated side-by-side in the genome.

Genome-wide repeats

Repeats that appear in multiple locations across the genome.

Paired-end reads

Sequencing technique that reads both ends of a DNA fragment to enhance assembly accuracy.

PCR amplification

A method to rapidly clone and amplify target DNA sequences for high-throughput sequencing.

Genomic library

A collection of DNA fragments that represent the entire genome stored separately.

Cloning

The process of copying DNA fragments into vectors for storage and analysis.

Microtiter well

A small container used to store cloned DNA fragments in genomic libraries.

Accuracy

The degree of correctness in genome assembly, important for reliable sequencing.

Cost Comparison

Analysis of expenses related to different sequencing methods, with clone-contig being more expensive.

Orientation

The correct positioning of genomic sequences as guided by genomic maps.

Verification

The process of confirming correct assembly of genome sequences.

Ground-truth checks

Validation processes that ensure genomic markers align with expected locations.

Map-first approach

Sequencing strategy that uses genomic maps prior to sequencing to guide assembly.

Sequence-first approach

Sequencing method that validates assembly after data has been collected.

Repetitive regions

Segments of the genome that are prone to errors during sequencing due to duplications.

Modern genomics

The cutting-edge field of study focused on genome sequencing, analysis, and manipulation.

DNA fragments

Smaller pieces of DNA that are sequenced and assembled to reconstruct the genome.

Computational assembly

The use of computer algorithms to piece together sequenced DNA fragments.

Image stitching analogy

The comparison of genomic assembly to stitching together overlapping images for coherence.

SNP

Single nucleotide polymorphism, a common type of genetic variation among individuals.