KEGG Pathway Database

Primary Databases

• GenBank is a repository of known nucleotide sequences with a flat file structure, readable by humans and computers.
• GenBank files contain information such as accession numbers, gene names, phylogenetic classification, and references to published literature.
• GenBank has transitioned from a flat file format to a more complex structure using XML and ASN.1 formats for improved manageability and data exchange.
• GenBank is an open-access sequence database that coordinates with individual laboratories and other sequence databases like EMBL and DDBJ.
• GenBank is an annotated collection of all nucleotide sequences available to the public.

GenBank Structure

• The nucleotide database is divided into three databases at NCBI: CoreNucleotide database, Expressed Sequence Tag (EST), and Genome Survey Sequence (GSS).
• CoreNucleotide database has most of the nucleotide sequences used and encloses all nucleotide records not in EST and GSS databases.

Submission to GenBank

• Sequences can be submitted to GenBank using BankIt, Sequin, and tbl2asn tools.

KEGG Pathway Database

• The KEGG Pathway database offers features to explore biosynthesis pathways, including search function, pathway maps, and data links.
• Pathway maps provide detailed information on molecules, enzymes, and genes involved in each step.
• Data links access relevant databases for genes, proteins, and other molecules associated with the pathway.

ViruSite Database

• ViruSite is a comprehensive database designed for viral genomics, integrating information on viral genomes, genes, and proteins from various sources.
• ViruSite incorporates all genomes from viruses, viroids, and satellites deposited in the NCBI Reference Sequence Database (RefSeq).
• Data from numerous resources like NCBI RefSeq, UniProtKB, Gene Ontology (GO), ViralZone, and PubMed are computationally extracted and integrated under human supervision.
• ViruSite offers an intuitive and user-friendly interface for easy navigation and exploration.

Gene Annotation

• Gene annotation involves analyzing the sequence and predicting its potential functions, adding valuable information to databases.
• Benefits of gene annotation include identifying genes and their locations, predicting gene function, providing insights into gene regulation and expression, and understanding biological processes and diseases.

Sequence Analysis Pipeline

• The pipeline involves pre-processing, gene prediction, functional annotation, structural annotation, integration, and visualization, quality assessment, and database submission.
• Each step involves specific tools and techniques, including quality control, sequence assembly, identifying ORFs, predicting coding regions, protein homology, domain prediction, GO annotation, and pathway mapping.

Accession Numbers

• Accession numbers are unique identifiers that permanently identify sequences in the database.

Primary vs. Secondary Databases

• Primary databases store raw, uninterpreted experimental data, while secondary databases provide a more comprehensive view of biological information with interpretations, annotations, and functionalities for exploring relationships and functions.
• Examples of primary databases include GenBank, DDBJ, and EMBL, while secondary databases include KEGG Pathway Database and ViruSite.

Types of Sequence Alignment

• Pairwise sequence alignment involves aligning two sequences to identify the optimal pairing, based on a scoring system that assigns positive scores to matching characters and negative scores to mismatching characters or gaps.
• Multiple sequence alignment involves aligning three or more sequences to identify conserved regions and reconstruct evolutionary relationships.
• Methods of pairwise sequence alignment include dot-matrix method, dynamic programming, and word or k-tuple method.
• Methods of multiple sequence alignment include exhaustive algorithms and heuristic algorithms.
• Applications of sequence alignment include identifying functional regions, understanding evolutionary relationships, and predicting protein structure and function.