Lecture 1: Biological Databases and Sequence Terminology

Vocabulary flashcards covering biological sequence databases (NCBI, EMBL, DDBJ, UniProtKB, Swiss-Prot, PIR), sequence terminology (ESTs, STSs, GSSs, HTG, HTC), database curation formats, and protein structural annotation case studies from the lecture.

NCBI

National Centre for Biotechnology Information; founded in 1988 and responsible since 1992 for the public accessibility of GenBank.

EMBL

European Molecular Biology Laboratory; a major European organization maintaining core nucleotide sequence data that partnered with Swiss-Prot in 1987.

DDBJ

DNA Data Bank of Japan; one of the three primary international nucleotide sequence repositories collaborating to mirror sequence data.

SWISS-PROT

A curated protein sequence database established in 1985 by the Swiss Institute of Bioinformatics and joined by EMBL in 1987.

RCSB PDB

Research Collaboratory for Structural Bioinformatics Protein Data Bank; a major structural database archiving 3D biological macromolecular structures.

InterPro

A protein database and resource providing functional analysis by classifying proteins into families and predicting domains and important sites.

MolMovDB

Protein Motion Database; a database dedicated to recording and illustrating macromolecular movements and conformational flexibility.

SCOP

Structural Classification of Proteins; a database categorizing protein structural domains based on their structural and evolutionary relationships.

CCDC

Cambridge Crystallographic Data Centre; a repository and organization dedicated to small-molecule crystal structure data.

Unannotated Sequence

Sequence entries in a database that have not yet had a FEATURE table added and have not been reviewed or touched by a human curator.

Synthetic Sequences

Man-made or engineered DNA sequences that have been artificially constructed in a laboratory, such as plasmids and BACs.

EST (Expressed Sequence Tag)

Short sequence reads derived from cDNA that was synthesized from mRNA templates using reverse transcriptase.

STSs (Sequence Tagged Sites)

Short, unique genomic sequence segments of known location used as physical markers for chromosome mapping.

GSSs (Genome Survey Sequences)

Short, single-pass genomic sequences used primarily to map and survey uncharacterized genomic regions.

HTC

High Throughput cDNA sequences; nucleotide database divisions designated for large-scale cDNA sequencing projects.

HTG

High Throughput Genomic sequences; unfinished large contigs generated by sequencing facilities that have not yet been finished and will contain sequencing errors.

Accession Number

A permanent, unique alphanumeric tag assigned to every entry in a database to index and present data manageably, analogous to a bench number.

UniProtKB

Universal Protein Resource Knowledgebase; a comprehensive protein resource formed in 2002 by the merger of Swiss-Prot, TrEMBL, and PIR.

PIR

Protein Information Resource; a public protein database that fused with Swiss-Prot and TrEMBL in 2002 to create UniProtKB.

Core Data (Protein Database)

The three essential foundational elements required for each protein record in UniProtKB: sequence data, bibliographic references, and taxonomic data.

Protein Annotations

Curated biological attributes associated with a sequence record, including protein functions, post-translational modifications, domains, sites, secondary/quaternary structures, similarities, variants, and disease associations.

Wellcome Trust Sanger Institute Sequencing Facility

A high-capacity genome sequencing operation characterized by 19 project-focused teams (such as shotgun and pathogen sequencing) and a production facility of 41 scientists operating in 4 shifts.

SRY (Sex-determining Region Y)

A transcriptional regulator encoded on the human Y chromosome that acts as a genetic switch to trigger male sex determination by directing pre-Sertoli cells to develop into Sertoli cells.

HMG Box

A conserved 69-amino-acid DNA-binding region (positions 60–128 in human SRY) that binds the minor groove via partial intercalation and induces DNA bending.

46,XY Sex Reversal 1 (SRXY1)

A clinical condition resulting from SRY gene mutations characterized by male-to-female sex reversal in individuals with a normal 46,XY karyotype, resulting in fibrous streak gonads.