Biological Databases and Genomic Resources

Vocabulary practice flashcards covering primary biological databases, protein domain and structural repositories, functional ontologies, and genome projects from Lecture 2.

Major DNA Databases

The primary international nucleotide sequence repositories that exchange data daily:

1. NCBI (GenBank/RefSeq) in the United States

2. EBI (EMBL) in Europe

3. DDBJ in Japan.

UniProtKB

The central protein sequence database, divided into:

1. Swiss-Prot (manually annotated, peer-reviewed records)

2. TrEMBL (automatically translated, computationally analyzed, uncurated records)

3. PIR

RCSB PDB (Protein Data Bank)

A structural database established in 1971 by the Research Collaboratory for Structural Bioinformatics for the collection, curation, and distribution of 3D macromolecular structures of proteins and nucleic acids.

PDB Entry Contents

The standard components of a structural record in the PDB include:

• a 3D structure summary

• experimental methods and parameters

• primary sequence data

• exact atomic geometry and coordinates.

InterPro

An integrated database for protein sequence analysis and classification that documents protein families, functional domains, and important sites by combining multiple partner databases.

PROSITE

A protein sequence motif method and database that identifies functional sites and domain signatures using regular expression patterns and sequence profiles.

Pfam

A large collection of protein families and domains identified by multiple sequence alignments and hidden Markov models (HMMs).

Pfam-A

The high-quality, manually curated section of the Pfam database, featuring curated seed alignments and hidden Markov models.

Pfam-B

The automated, uncurated partition of the Pfam database generated through automated domain prediction methods to supplement Pfam-A coverage.

PRINTS - protein domain

A diagnostic sequence motif database based on protein fingerprints, which are groups of conserved motifs excised from sequence alignments to characterize a protein family.

ProDom

A protein domain database generated automatically from sequence cluster methods using PSI-BLAST comparisons.

HMM Logo - Pfam

A graphical representation used to visualize profile hidden Markov models, showing consensus sequences and the relative frequency of amino acids at each residue position.

HMG-box (High Mobility Group Box)

A protein domain consisting of three alpha helices separated by loops that binds specifically to non-B-type (kinked or unwound) DNA conformations with high affinity and induces DNA bending.

Gene Ontology (GO) Project

A collaborative initiative providing a controlled, standardized vocabulary (ontology) to describe gene product characteristics and functions consistently across organisms.

Three GO Ontologies

The three defined domains used to classify gene products in Gene Ontology:

1. Molecular Function

2. Biological Process

3. Cellular Component.

Directed Acyclic Graph (DAG) - GO context

The hierarchical data structure used by Gene Ontology where terms can have multiple parent categories without forming circular loops.

OMIM (Online Mendelian Inheritance in Man)

An online catalog of human genes and genetic disorders containing phenotypic descriptions, gene mappings, clinical synopses, and disease histories.

KEGG (Kyoto Encyclopedia of Genes and Genomes)

A bioinformatics knowledge base integrating genomic, chemical, and systemic functional information, including molecular wiring diagrams and metabolic pathway maps.

Enzyme Commission (EC) Number - (KEGG)

A four-digit numerical classification scheme for enzymes in pathway databases like KEGG that identifies the specific catalyzed biochemical reaction and pathway location.

Fluorouracil (5-FU) - KEGG

A pyrimidine analog antineoplastic antimetabolite drug that exerts anticancer effects through the inhibition of thymidylate synthase (TYMS) in pyrimidine metabolism.

DrugBank - link though KEGG

A bioinformatics and cheminformatics database combining comprehensive drug chemical and pharmacology data with detailed drug target and enzyme information.

FlyBase

An organism-specific genetic and genomic database dedicated to Drosophila melanogaster and related fly species.

WormBase

An organism-specific database dedicated to the genetics, genomics, and biology of the nematode Caenorhabditis elegans and related nematodes.

TAIR (The Arabidopsis Information Resource)

An organism-specific database providing genetic and molecular biology data for the model flowering plant Arabidopsis thaliana.

SilkDB

A specialized genomic database for the silkworm, Bombyx mori, providing functional annotations, chromosomal mapping, ESTs, and microarray expression profiles.

Earth BioGenome Project (EBP) - large scale

A large-scale initiative aiming to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of ten years.

Uncurated Sequence Repository

A public archival repository (e.g., primary GenBank patent entries) where submitted DNA data remains unedited and permanently online regardless of length or validity until removed by the submitter.

Protein DOMAIN databases

1. Interpro

2. Pfam (A & B)

3. Prosite

Cluster vs Motif sequence in Portein DOMAIN

Motif:

• Pfam

• prosite

• PRINT

CLUSTER:

• prodom

Protein STRUCTURAL

1. PDB (protein data bank)

2. SCOP

3. CCDC - crystal

Other databases

1. GO - gene ontology

2. KEGG - kyoto encyclopedia of Genome

3. OMIM - online mandelian inheritance of man

4. COG