lec 15-Genetics and Molecular Biology: Genomics and Bioinformatics

Vocabulary-style flashcards covering the definitions, history, technologies, and applications of genomics and bioinformatics based on the lecture material.

Genomics

The study of genomes—specifically its genetic material—and how that information translates to function.

Bioinformatics

The use of mathematics, statistics, and computer science to better understand the genome.

Sanger Sequencing

A sequencing method used in 1977 to sequence the first DNA-based genome, $\phi X174$.

Polymerase Chain Reaction (PCR)

A molecular biology technique invented in 1983 used to amplify segments of DNA.

Next Generation Sequencing (NGS)

Technologies launched around 2007 that enable experiments producing millions of short DNA reads.

Long read sequencing

Sequencing technologies, such as Nanopore and PacBio, introduced around 2014 that are essential for filling gaps in complex genomic regions like centromeres and telomeres.

Pangenome

A collection of human genome reference sequences used to represent diversity, moving away from a single reference genome based on a blended ancestry.

Gene annotation

The use of computer programs to identify protein-coding genes, exons, introns, and regulatory sites like the TATA box ($TATA(A/T)A(A/T)$) within a genome.

Open Reading Frames (ORFs)

DNA sequences that have the potential to be translated into protein, which software models detect to annotate genomes.

FASTA

A text-based bioinformatics file format used for representing nucleotide or peptide sequences with a header line.

FASTQ

A bioinformatics file format that contains sequencing data from machines like Illumina, including both the sequence and quality scores.

BLAST

A heuristic algorithm used for fast fuzzy searching to identify similar but not identical sequences within large genomic databases.

ENCODE (Encyclopedia of DNA Elements)

A large-scale collaborative project aimed at decrypting the function of the genome by mapping transcription factor binding sites, epigenetic modifications, and 3D contacts.

Position Weight Matrices (PWMs)

Models used to represent the specific DNA sequence motifs targeted and bound by transcription factors.

Bedtools

A suite of bioinformatics tools designed for the manipulation and combination of genomic intervals.

CLUSTAL Omega

A multiple alignment software used to identify conserved regions and functional domains in DNA or protein sequences across different species.

Needleman–Wunsch

An alignment algorithm that finds the best global alignment between two sequences by computing a complete matrix.

Smith–Waterman

An alignment algorithm that finds the best local alignment between sequences.

Gene Ontology

A hierarchical classification of known genes according to dimensions such as biological process, molecular function, and cellular context.

Ancient DNA (aDNA)

Fragments of DNA recovered from extinct species; calculations and corrections are required due to chemical degradation and damage over time.

Metagenomics

The study of genetic material recovered directly from environmental samples (like soil or gut) to identify organisms that cannot be grown in a lab.

GWAS (Genome-wide Association Study)

A statistical framework used to analyze massive amounts of genomic data to identify loci linked to specific phenotypes or diseases.

Xena

A shared database and web interface that makes cancer genomics data freely accessible to researchers worldwide.