Biological Databases and Genome Browsers: Comprehensive Study Notes

Core Public DNA Databases

• There are three major public DNA databases that share data so that their underlying raw DNA sequences are identical. These databases include:     * GenBank: Housed at the National Center for Biotechnology Information (NCBI) in the United States.     * EMBL (European Molecular Biology Laboratory): Housed at the European Bioinformatics Institute (EBI).     * DDBJ (DNA Data Bank of Japan): Housed in Japan.

Taxonomy Statistics at NCBI (Historical Growth to 2026)

• October 2011 Data: Over $200,000$ species represented in GenBank.     * Archaea: Higher taxa: $108$, Genus: $128$, Species: $705$, Lower taxa: $202$, Total: $1,143$.     * Bacteria: Higher taxa: $1,150$, Genus: $2,144$, Species: $11,699$, Lower taxa: $11,951$, Total: $26,944$.     * Eukaryota: Higher taxa: $17,972$, Genus: $55,940$, Species: $229,074$, Lower taxa: $19,636$, Total: $322,618$.     * Fungi: Higher taxa: $1,289$, Genus: $3,885$, Species: $24,104$, Lower taxa: $1,809$, Total: $31,083$.     * Metazoa: Higher taxa: $13,117$, Genus: $36,024$, Species: $105,591$, Lower taxa: $9,075$, Total: $163,807$.     * Viridiplantae: Higher taxa: $2,155$, Genus: $13,643$, Species: $91,331$, Lower taxa: $7,434$, Total: $114,563$.     * Viruses: Higher taxa: $524$, Genus: $358$, Species: $8,313$, Lower taxa: $70,978$, Total: $80,173$.     * All Taxa Total: Higher taxa: $19,779$, Genus: $58,571$, Species: $255,857$, Lower taxa: $102,802$, Total: $437,012$.

• January 2015 Data: Over $300,000$ species represented.     * All Taxa Total: Higher taxa: $22,925$, Genus: $72,475$, Species: $324,676$, Lower taxa: $23,896$, Total: $443,972$.

• January 2018 Data: Over $400,000$ species represented.     * All Taxa Total: Higher taxa: $26,376$, Genus: $84,399$, Species: $407,894$, Lower taxa: $28,859$, Total: $547,528$.

• January 2021 Data: Over $487,000$ species represented.     * All Taxa Total: Higher taxa: $67,914$, Genus: $96,575$, Species: $487,619$, Lower taxa: $33,764$, Total: $685,872$.

• January 2024 Data: Over $566,000$ species represented.     * All Taxa Total: Higher taxa: $78,140$, Genus: $108,319$, Species: $566,976$, Lower taxa: $39,649$, Total: $793,084$.

• January 2026 Forecast: Over $618,000$ species represented.     * All Taxa Total: Higher taxa: $142$, Genus: $77$, Species: $618,410$, Lower taxa: $659,633$, Total: $660,279$.

National Center for Biotechnology Information (NCBI) Key Features

• Mission: NCBI advances science and health by providing access to biomedical and genomic information.

• PubMed:     * The National Library of Medicine's (NLM) search service.     * Contains over $39$ million citations in MEDLINE (as of Jan 2026).     * Provides links to online journals and PubMed Central.

• Search and Retrieval System Integration: The NCBI system integrates data across various domains, including:     * Scientific literature (PubMed).     * DNA and protein sequence databases.     * Conserved protein domains and protein family models.     * Gene expression datasets (GEO DataSets and GEO Profiles).     * $3D$ protein structure data.     * PopSet: Sequence sets from phylogenetic and population studies.     * Assemblies of complete genomes and sequence reads (SRA).     * Taxonomic classification and nomenclature.     * Clinical datasets (ClinVar, dbVar, GTR).     * OMIM (Online Mendelian Inheritance in Man): A catalog of human genes and genetic disorders created by Dr. Victor McKusick and led by Dr. Ada Hamosh at JHMI.     * Chemical information and pathway data (PubChem: BioAssays, Compounds, Substances).

• BLAST (Basic Local Alignment Search Tool):     * NCBI's primary sequence similarity search tool.     * Supports analysis for both DNA and protein databases.     * Executes over $100,000$ searches per day.     * Common tools include blastn (nucleotide), blastp (protein), blastx (translated nucleotide query against protein database), and tblastn (protein query against translated nucleotide database).

• Taxonomy Database:     * Features a browser for major divisions of life: Archaea, Bacteria, Eukaryota, and Viruses.     * Provides genetic codes and molecular data on extinct organisms.     * Useful for identifying proteins or genes from specific species.

• Structure (Molecular Modeling Database):     * Contains biopolymer structures derived from the Protein Data Bank (PDB).     * Cn3D: A visualization tool for $3D$ structures.     * iCn3D: A WebGL-based viewer for interactive, web-based viewing of macromolecular structures.     * VAST (Vector Alignment Search Tool): Used to identify similar protein $3D$ structures.

Accession Numbers and Identifiers

• Definition: An accession number is a label (a string of letters and/or numbers) used to identify a specific molecular sequence record.

• Examples (for Beta Globin, HBB):     * U01317.1: GenBank genomic DNA sequence.     * NG_000007.3: RefSeqGene identifier.     * rs192792910: dbSNP identifier for a single nucleotide polymorphism.     * AA970968.1: Expressed sequence tag (EST).     * NM_000518.4: RefSeq DNA sequence corresponding to a transcript (mRNA).     * NP_000509.1: RefSeq protein identifier.     * CAA00182.1: GenBank protein identifier.     * Q14473: SwissProt protein identifier.     * 1YE0|B: Protein Data Bank (PDB) structure record.

• RefSeq Project (NCBI):     * Expertly curated, stable reference versions of sequences.     * NC_######: Complete genome or chromosome.     * NT_######: Genomic contig.     * NM_######: mRNA (DNA format).     * NP_######: Protein.

Case Study: Beta Globin (HBB) Database Search

• NCBI Gene Entry (ID: 3043):     * Official Symbol: HBB.     * Description: Hemoglobin subunit beta [Homo sapiens (human)].     * Location: Chromosome $11$, $NC_000011.10$ ($5,225,464..5,227,071$, complement).     * Summary: HBA (alpha) and HBB (beta) loci determine the two polypeptide chains in adult hemoglobin (Hb A). Mutations in beta globin cause sickle cell anemia, while absences or reductions cause thalassemias ($beta-zero-thalassemia$ and $beta-plus-thalassemia$).     * Locus Order: $5'- ext{epsilon--gamma-G--gamma-A--delta--beta}-3'$.     * GeneRIFs (Gene References Into Functions): Examples include validation of target genes for HbF and HbA2 levels, HBB as a biomarker for lung cancer, and novel thalassemia mutations.     * Pathways: Involved in $O_2/CO_2$ exchange in erythrocytes and scavenging of heme from plasma.

• NCBI Protein Entry (NP_000509.1):     * Length: $147$ aa.     * Source: Homo sapiens.     * Features: Includes specific sites like hemoglobin beta-like conserved domains and microbial infection cleavage sites (by N. americanus apr-2 at residues $129..130$, $141..142$, and $145..146$).

Amino Acid One-Letter Code Reference

• A: Alanine (Ala)

• R: Arginine (Arg)

• N: Asparagine (Asn)

• D: Aspartic acid (Asp)

• C: Cysteine (Cys)

• E: Glutamic Acid (Glu)

• Q: Glutamine (Gln)

• G: Glycine (Gly)

• H: Histidine (His)

• I: Isoleucine (Ile)

• L: Leucine (Leu)

• K: Lysine (Lys)

• M: Methionine (Met)

• F: Phenylalanine (Phe)

• P: Proline (Pro)

• S: Serine (Ser)

• T: Threonine (Thr)

• W: Tryptophan (Trp)

• Y: Tyrosine (Tyr)

• V: Valine (Val)

Genome Browsers

• General Characteristics:     * Display ideograms of chromosomes with annotation tracks (user-selected data layers).     * Crucial for visualizing genomic DNA organization.

• Ensembl (www.ensembl.org):     * Focuses on vertebrate genomes.     * Integrates comparative genomics, evolution, variation, and regulation.     * Tools include BioMart (exporting custom datasets) and VEP (Variant Effect Predictor).     * Latest version mentioned: Release $113$ (October 2024).

• UCSC Genome Browser:     * Focuses on humans and other eukaryotes.     * Supports different assembly versions (e.g., hg18, hg19, or hg38).     * Display Modes: Tracks can be set to hide, dense, squish, pack, or full.     * UCSC Table Browser: Qualitative tool for retrieving tabular genomic data. Can output in formats like BED or sequence data.

Practical Exercise: Finding SNPs in Coding Exons on Chromosome 11

• Step 1: Use UCSC Table Browser. Set group to "Variation," track to "dbSNP 155," and position to "chr11."

• Step 2: Set output format to BED and select the checkbox "Send query to Galaxy."

• Step 3: In Galaxy, rename the dataset to "SNPs."

• Step 4: Return to UCSC Table Browser to get coding exons. Set group to "Genes and Gene Predictions" and track to "NCBI RefSeq." Set the output option to "Coding Exons" and send to Galaxy.

• Step 5: In Galaxy, use the tool "Operate on Genomic Intervals."

• Step 6: Select "Intersect the intervals of two datasets." Choose the "SNPs" dataset and the "coding exons" dataset.

• Step 7: Run the tool and view the results to find the total count of SNPs located specifically within the coding exons of chromosome $11$.