Unit 3.

Biological Sequence Databases: National Center for Biotechnology Information

(NCBI): Tools and Databases of NCBI, Database Retrieval Tool, Sequence Submission to
NCBI, Basic local alignment search tool (BLAST), Nucleotide Database, Protein Database,
Gene Expression Database.

The National Center for Biotechnology Information (NCBI) is a branch of the U.S.
National Library of Medicine (NLM) located within the National Institutes of Health (NIH).
It plays a central role in advancing biomedical research and supporting healthcare by
providing access to a wide range of biological information. The functions and services of
NCBI include:

1. NCBI hosts databases like PubMed (for scientific literature), GenBank (for DNA
sequences), and Gene (for gene-specific information). These databases are essential
for researchers worldwide.
2. NCBI provides a variety of tools for sequence analysis, including BLAST (Basic
Local Alignment Search Tool) for comparing biological sequences, and Primer-
BLAST for designing primers for PCR experiments.
3. It supports tools for the analysis of genomic, transcriptomic, and proteomic data,
which are crucial for understanding biological systems and advancing personalized
medicine.
4. NCBI provides tutorials, documentation, and webinars to help researchers utilize its
tools and databases effectively.
5. NCBI promotes open access to scientific data, making it easier for scientists and the
public to access important research findings.

NCBI is a vital resource for scientists, healthcare professionals, and educators in the
fields of biotechnology, genomics, and bioinformatics. If you need specific information or
help with any of their resources, feel free to ask!

Tools and Databases of NCBI: The NCBI provides a wide array of tools and databases for
researchers and scientists in fields like genomics, bioinformatics, and molecular biology.

A. Databases: NCBI maintains many databases for accessing biological and biomedical
data. some of the most widely used databases are -

a. GenBank: GenBank is one of the most important and widely used resources provided
by the National Center for Biotechnology Information (NCBI). It is a publicly
accessible nucleotide sequence database that houses an extensive collection of genetic
information from a wide variety of organisms. Researchers from around the world
submit their DNA and RNA sequence data to GenBank, making it a key resource for
genomic research.

Key Features of GenBank

1. GenBank holds nucleotide sequences from a diverse range of organisms, including

humans, plants, animals, microbes, viruses, and more.
2. GenBank is open access, meaning anyone can search, retrieve, and download
sequence data for free. It is crucial for bioinformatics and genomic research, as
 scientists rely on this data for studies on gene function, evolutionary biology, disease
mechanisms, and more.
3. Researchers submit their sequence data to GenBank, where it is stored and made
available to the public.
4. GenBank provides functional annotations that describe the role and significance of
genes, coding regions, and other elements in the genome.
5. GenBank is linked to other NCBI databases like PubMed, PubChem, and the Gene
database, making it easier to find related publications, proteins, and chemical data
associated with the sequences.
6. GenBank is integrated with NCBI's Entrez search system, which enables users to
search across multiple NCBI databases simultaneously.
7. Tools like BLAST can be used to compare sequences against GenBank's vast
collection to find similarities and identify potential homologs.

GenBank Search Tools:

1. Entrez Nucleotide Database: This is the primary tool for searching GenBank’s
nucleotide sequences. Users can search by gene name, organism, sequence accession
number, or other keywords.
2. BLAST: A sequence comparison tool that allows you to search GenBank to find
sequences that are similar to your query sequence.
3. GenBank Flat Files: GenBank data can be downloaded in bulk or in smaller sets in
flat-file formats for local analysis.
4. Genome Data Viewer: A tool for visualizing genome data, including sequences
stored in GenBank.

Importance:

1. GenBank is one of the largest and most comprehensive publicly available

nucleotide databases.
2. It plays a critical role in fostering collaboration among researchers globally, as
it provides easy access to a shared repository of sequence data.
3. GenBank provides the genetic sequences needed to explore gene function,
genetic diversity, and evolutionary relationships.
4. Researchers can use GenBank data to identify and characterize disease-
causing mutations, study pathogens, and develop diagnostics.
5. Pharmaceutical researchers use GenBank to identify new drug targets,
especially through the study of genes associated with disease.
6. By comparing sequences from different species, researchers can gain insights
into evolutionary processes and common ancestry.

b. PubMed: It is one of the most important and widely used resources for accessing
scientific literature in the fields of biomedicine, life sciences, and healthcare. It is a
free resource maintained by the National Center for Biotechnology Information
(NCBI), a branch of the U.S. National Library of Medicine (NLM).

PubMed contains millions of references (citations) from biomedical and life science
journals, including fields like medicine, genetics, molecular biology, pharmacology, and
 public health. PubMed provides abstracts, citations, and metadata (such as authors,
publication dates, journals) for each article. PubMed allows users to perform advanced
searches using keywords, authors, journal names, publication dates, and more. PubMed
integrates with various citation management tools, such as EndNote, Zotero, and
RefWorks, making it easy to organize and cite references for research projects or
publications.

How to Use PubMed: In the PubMed search bar, simply enter keywords related to your
topic of interest (e.g., “diabetes treatment” or “cancer genetics”).

c. Gene: The Gene database is one of the essential resources provided by the National
Center for Biotechnology Information (NCBI). It provides comprehensive
information on genes across a variety of organisms, including humans, plants,
animals, and microbes. Researchers use the Gene database to study gene structure,
function, and associated diseases. The Gene database includes gene data for a wide
range of species, from humans to bacteria and other model organisms.

It provides detailed annotations about each gene, including its function, expression
patterns, and relationships to diseases. The database offers descriptions of gene functions
based on experimental data and computational predictions. To search for a specific gene, you
can simply enter the gene's name, symbol, or synonym into the search bar on the Gene
database homepage.

d. SNP (Single Nucleotide Polymorphism): A database of human genetic variations.

Focuses on single nucleotide polymorphisms (SNPs), which can play a role in
diseases, traits, and drug responses.
e. PubChem: A chemical information resource. Contains information on the biological
activities of small molecules and provides tools to search for chemical structure,
properties, and bioactivity.
f. RefSeq (Reference Sequence): Provides a curated collection of sequences
representing reference standards for genomes, transcripts, and proteins. It serves as a
standard for representing the reference sequences for genes, proteins, and genomes,
and it plays a critical role in various biological research applications, including gene
annotation, mutation analysis, and comparative genomics. RefSeq provides highly
curated and comprehensive reference sequences for genomic data, mRNA transcripts,
and protein sequences. Unlike other sequence databases like GenBank, which include
all submitted sequences, RefSeq offers carefully curated and verified sequences.
These sequences are the result of manual annotation and computational methods to
ensure accuracy. It helps researchers study gene function, protein structure, and
genetic variation.

B. Tools: NCBI also provides several bioinformatics tools for data analysis, sequence
comparison, and visualization.

BLAST (Basic Local Alignment Search Tool): Helps researchers compare sequences
against a database to find similarities and understand evolutionary relationships. Includes
several variations such as:

BLASTn (nucleotide sequences)

 BLASTp (protein sequences)

BLASTx (translated nucleotide to protein)

TBLASTn (protein to translated nucleotide)

Entrez: Provides a unified interface to search across various NCBI databases (e.g., PubMed,
GenBank, Gene, etc.), allowing users to access integrated biological data.

Primer-BLAST: Used for designing primers for PCR (Polymerase Chain Reaction)
experiments. It ensures specificity to the target region while minimizing non-specific binding.

GeneRIF (Gene Reference Into Function) Each entry includes a summary of the function
or disease association of the gene, drawn from scientific literature.

BLAST+: An advanced version of BLAST. Allows command-line access to BLAST, which

is suitable for large-scale data analysis and automated tasks.

Taxonomy Browser: Tool for exploring the biological classification of organisms.