Bioinformatics & Genomics Vocabulary Flashcards

A set of vocabulary flashcards key concepts in Bioinformatics & Genomics (Modules 1-6).

dNTPs

Deoxyribonucleoside triphosphates (A, C, G, T) that serve as the fundamental building blocks of DNA.

NTPs

Ribonucleoside triphosphates (A, C, G, U) that serve as the fundamental building blocks of RNA.

Sequence Alignment

Arranging nucleotide or amino acid sequences with gaps to identify conserved positions, point mutations, indels, and homology.

Universal Genetic Code

The system where identical triplet codons encode identical amino acids across virtually all life, utilizing AUG as the start codon and UAA, UAG, and UGA as stop codons.

Sickle Cell Anemia

A condition caused by a single missense mutation in hemoglobin resulting in strand aggregation, red blood cell sickling, and capillary blockage.

GenBank

A primary archival nucleotide database founded in 1981 by NCBI that stores raw direct-submission DNA and cDNA.

INSDC

The International Nucleotide Sequence Database Collaboration formed by GenBank, ENA, and DDBJ to synchronize and share global sequence submissions daily.

RefSeq

A non-redundant, manually curated wild-type reference standard database containing DNA, RNA, and protein sequences without duplicates.

UniProtKB

A curated protein sequence database containing functional, structural, active site, and domain annotations.

Orthologs

Homologous genes in different species derived from a speciation event that perform the same function.

Paralogs

Homologous genes created by gene duplication within a genome that evolve divergent functions.

Exon Shuffling

The duplication and mobilization of exons via retrotransposons to create modular proteins with shared domains.

Vertical Gene Transfer

The transmission of genetic material directly from parent to offspring via reproduction.

Horizontal Gene Transfer

The direct non-reproductive transfer of DNA between different organisms.

Germ Cell Mutations

Heritable mutations in sperm or egg cells passed to offspring somatic cells that predispose individuals to familial syndromes.

BLAST Heuristic Search

A search mechanism that generates query words $\ge T$, finds exact database hits, extends bidirectionally until the score decays, and trims high-scoring segment pairs (HSPs).

E-value

In BLAST, a metric representing random chance matches where values near zero indicate statistically significant sequence similarity.

PSI-BLAST

An iterative search program that constructs a Position-Specific Scoring Matrix (PSSM) to identify distant protein homologs.

Multiple Sequence Alignment (MSA)

The alignment of $\ge 3$ biological sequences with gaps to identify conserved active sites, structural motifs, and ancestry.

Protein Data Bank (PDB)

A structural repository storing 3D atomic coordinates, atom identities, residues, occupancies, and B-factors of biological macromolecules.

NMR Spectroscopy

A structural biology technique utilizing nuclear spin resonance to determine structures of soluble proteins smaller than $30\,\text{kDa}$.

Molecular Clock

An evolutionary model assuming sequences substitute at roughly constant rates, allowing divergence time $t$ to be calculated via $r = \frac{K}{2t}$ with fossil calibration.

TP53 Gene

A gene encoding a transcription factor activated by DNA damage to halt the cell cycle for repair, apoptosis, or senescence, with over $90\%$ of cancer mutations hitting its DNA-binding domain.