Bioinformatics and Genomics Vocabulary

Comprehensive vocabulary flashcards covering key terms across Modules 1 through 6 of Bioinformatics and Genomics.

dNTPs

Deoxyribonucleotides (adenine, guanine, cytosine, thymine) that serve as the fundamental building blocks of DNA.

NTPs

Ribonucleotides (adenine, guanine, cytosine, uracil) that serve as the fundamental building blocks of RNA.

Sequence Alignment

The computational matching or arrangement of biological sequences with gaps to identify conserved positions, point mutations, indels, and infer homology or common ancestry.

Primary Structure

The linear amino acid sequence of a polypeptide chain read from the N-terminal to the C-terminal direction.

Secondary Structure

Localized conformations of a polypeptide chain, such as $\beta$-sheets and $\beta$-sheets, stabilized by non-covalent interactions.

Tertiary Structure

The complete 3D folding of a single polypeptide chain, maintained by non-covalent interactions and covalent disulfide bonds.

Quaternary Structure

The multi-subunit assembly formed when multiple folded polypeptide chains combine into a functional complex.

Universal Genetic Code

The principle that identical triplet mRNA codons dictate the exact same amino acids across virtually all life, initiated by start codon AUG (methionine) and terminated by stop codons UAA, UAG, or UGA.

Sickle Cell Anemia Mutation

A single missense mutation in the hemoglobin gene altering a single amino acid, causing rigid strand aggregation, erythrocyte sickling, and capillary occlusion.

TP53 Gene

A tumor suppressor gene coding for the p53 nuclear transcription factor, which activates upon cellular stress or DNA damage to halt cell division for DNA repair, apoptosis, or senescence.

GenBank

The primary archival nucleotide database founded in 1981 by Walter Goad at NCBI to store directly submitted raw DNA and cDNA sequences.

INSDC

The International Nucleotide Sequence Database Collaboration, comprising GenBank, ENA, and DDBJ, which synchronizes and shares global sequence submissions daily.

Feature Keys

GenBank entry annotations (such as source, gene, mRNA, and CDS) that demarcate explicit sequence coordinates and provide detailed biological qualifiers.

RNA Splicing

The enzymatic excision of non-coding introns from precursor RNA transcripts to join coding exons into mature messenger RNA.

Alternative Splicing

A cellular mechanism that joins different combinations of exons from a single precursor RNA, yielding multiple distinct mRNA transcripts and protein isoforms from one gene.

Primary Database

An uncurated repository (such as GenBank, ENA, or DDBJ) storing directly submitted archival sequences that may contain errors and redundancies.

Secondary Database

A curated, non-redundant database (such as RefSeq, nr/nt, or UniProtKB) that filters, derives, and annotates reference datasets from primary archival entries.

RefSeq

A manually curated, non-redundant secondary database maintained by NCBI that provides wild-type reference standards for genomic DNA, RNA, and protein sequences.

UniProtKB

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

Positive Mutation

A heritable genetic change that confers an advantageous adaptation and increases evolutionary fitness.

Negative Mutation

A genetic change that disrupts essential biological functions or causes disease, thereby reducing evolutionary fitness.

Neutral Mutation

A genetic variation (such as a synonymous substitution) that exerts no effect on organismal survival or evolutionary fitness.

Homologs

Biological sequences or genes descended from a shared common ancestral sequence.

Orthologs

Homologous genes in different species that diverged due to a speciation event and typically retain identical functions.

Paralogs

Homologous genes within a single genome that arose via gene duplication events and often evolve divergent functions.

Exon Shuffling

A mechanism mediated by retrotransposons like LINE-1 where exons are duplicated or mobilized into non-homologous genes, creating modular proteins with shared domains.

Vertical Gene Transfer

The transmission of genetic material from parent to offspring through sexual or asexual reproduction.

Horizontal Gene Transfer

The direct non-reproductive transfer of genetic material between non-parental cells or different organisms.

Germ Cell Mutations

Heritable sequence alterations originating in sperm or egg precursor cells that are passed to all somatic cells of offspring, predisposing to inherited disorders.

TP53 DNA-Binding Domain Hotspot

The central core region of p53 (codons 100–300) where over 90% of cancer-associated mutations cluster, specifically targeting hotspot residues 175, 248, and 273.

BLAST

A heuristic local alignment search algorithm that finds exact query words at or above threshold $T$, extends them bidirectionally, and trims high-scoring segment pairs (HSPs).

E-value

The statistical expectation parameter in BLAST indicating the number of database matches expected purely by random chance; values near zero indicate high statistical significance.

Percent Identity

The fraction of exactly identical amino acid or nucleotide residues over an aligned sequence span, including gaps.

Similarity (Positives)

The fraction of aligned residues in a protein alignment possessing neutral or favorable substitution scores according to a scoring matrix.

BLASTp

A BLAST algorithm that compares an amino acid query sequence against a protein database.

BLASTn

A BLAST algorithm that compares a nucleotide query sequence against a nucleotide database.

BLASTx

A BLAST algorithm that translates a nucleotide query in all six reading frames to search against a protein database.

PSI-BLAST

An iterative BLAST program that builds position-specific scoring matrices (PSSMs) to detect distant evolutionary homologs.

Multiple Sequence Alignment (MSA)

The alignment of three or more homologous biological sequences with gaps to identify conserved active sites, structural motifs, and evolutionary ancestry.

ClustalW

A progressive multiple sequence alignment program that calculates distance matrices, builds guide trees, and aligns sequences annotated with conservation symbols (*, :, .).

Protein Data Bank (PDB)

The central worldwide repository storing 3D atomic coordinates, atom identities, amino acid residues, chain identifiers, occupancies, and B-factors.

X-ray Crystallography

An experimental technique determining atomic coordinates by collecting diffraction patterns from irradiated protein crystals and converting them into electron density maps.

NMR Spectroscopy

An experimental technique detecting nuclear spin resonance and chemical shifts in soluble proteins under $30\,\text{kDa}$ to determine 3D structure and solution dynamics.

Molecular Viewers

Software tools (such as Chimera) that read 3D coordinate PDB files to render interactive ribbon, surface, or CPK models and compute structural RMSD.

Ab Initio Structure Prediction

A computational structure prediction method evaluating thermodynamic energy configurations using physical principles without relying on solved template structures.

AlphaFold2

A deep learning, artificial neural network platform that utilizes multiple sequence alignments and coevolutionary constraints to predict highly accurate 3D tertiary protein structures.

Molecular Clock

The evolutionary principle that biological sequences substitute residues at a roughly constant rate, allowing divergence time $t$ to be calculated using $r = \frac{K}{2t}$.

Three Domains of Life

The primary evolutionary domains (Bacteria, Archaea, and Eukaryota) derived by Carl Woese, where Archaea and Eukaryota share a more recent sister ancestor than either does with Bacteria.

TP53 Gene Family

The paralogous gene group comprising p53, p63, and p73 that originated from ancient gene duplication events of a single common ancestral gene.