Bioinformatics is an interdisciplinary field that combines biology, computer science, statistics, and mathematics to study biological data. The amount of biological data generated in recent years is enormous, and it is impossible to manually analyze such data. Bioinformatics tools are used to store, process, analyze, and visualize large biological datasets. One of the most important resources for bioinformaticians is the National Center for Biotechnology Information (NCBI), which provides access to a vast amount of biological data and various bioinformatics tools. This article will provide a comprehensive guide to NCBI and its various resources.
Table of Contents
- Introduction
- What is NCBI?
- NCBI Resources
- PubMed
- GenBank
- RefSeq
- BLAST
- SRA
- How to Access NCBI Resources
- NCBI Tools
- Entrez
- Gene
- GEO
- Primer-BLAST
- Conserved Domain Database
- COBALT
- Cn3D
- NCBI Databases for Genomic Analysis
- Assembly
- Genome Data Viewer
- Variation Viewer
- Genome Workbench
- NCBI Education and Training Resources
- Conclusion
- FAQs
- What is NCBI used for?
- Is NCBI a free resource?
- Can I download data from NCBI?
- What is the best way to search for a gene sequence in NCBI?
- What are some of the bioinformatics tools available on NCBI?
1. Introduction
The National Center for Biotechnology Information (NCBI) is a part of the United States National Library of Medicine (NLM), which is a branch of the National Institutes of Health (NIH). NCBI is one of the most important resources for the field of bioinformatics, providing access to a vast amount of biological data and various bioinformatics tools. In this article, we will provide a comprehensive guide to NCBI and its various resources.
2. What is NCBI?
NCBI is a public, web-based resource that provides access to a vast amount of biological data and various bioinformatics tools. It was established in 1988 and is located in Bethesda, Maryland. NCBI’s primary mission is to provide access to biomedical and genomic information to researchers, clinicians, and the public. NCBI provides access to various databases, including PubMed, GenBank, and RefSeq, and various bioinformatics tools, including BLAST and Entrez.
3. NCBI Resources
NCBI provides access to various databases and resources that are useful for researchers in the field of bioinformatics. Some of the most important NCBI resources are discussed below.
3.1 PubMed
PubMed is a database of biomedical literature, including articles from various biomedical journals. PubMed includes over 30 million citations and abstracts of articles published in biomedical journals. PubMed is a free resource and can be accessed through the NCBI website.
3.2 GenBank
GenBank is a database of nucleotide sequences, including DNA and RNA sequences. GenBank includes sequences from various organisms, including bacteria, viruses, and eukaryotes. GenBank is a free resource and can be accessed through the NCBI website.
3.3 RefSeq
RefSeq is a database of annotated genomic, transcript, and protein sequences. RefSeq includes high-quality.
3.4 BLAST
BLAST (Basic Local Alignment Search Tool) is a sequence similarity search tool that allows users to compare their sequences with the sequences in the NCBI databases. BLAST can be used to identify homologous sequences, determine the function of a gene, and detect genetic variations. BLAST is a free resource and can be accessed through the NCBI website.
3.5 SRA
SRA (Sequence Read Archive) is a database of high-throughput sequencing data, including next-generation sequencing and third-generation sequencing data. SRA provides access to a vast amount of sequencing data, which can be used for various applications, including transcriptomics, genomics, and metagenomics. SRA is a free resource and can be accessed through the NCBI website.
4. How to Access NCBI Resources
NCBI resources can be accessed through the NCBI website (https://www.ncbi.nlm.nih.gov/). The NCBI website is user-friendly and provides various search options for different databases and resources. Users can search for specific sequences, genes, proteins, and literature using various search options, including text search, BLAST, and Entrez.
5. NCBI Tools
NCBI provides various bioinformatics tools that are useful for analyzing biological data. Some of the most important NCBI tools are discussed below.
5.1 Entrez
Entrez is a search and retrieval system that allows users to search multiple NCBI databases simultaneously. Entrez provides a user-friendly interface that allows users to search for specific sequences, genes, proteins, and literature using various search options, including text search, BLAST, and SRA.
5.2 Gene
Gene is a database that provides information about genes and their function, including gene sequences, genomic location, and related diseases. Gene also provides access to various tools, including gene expression analysis and gene variation analysis.
5.3 GEO
GEO (Gene Expression Omnibus) is a database of gene expression data, including microarray and next-generation sequencing data. GEO provides access to a vast amount of gene expression data, which can be used for various applications, including gene expression analysis, pathway analysis, and network analysis.
5.4 Primer-BLAST
Primer-BLAST is a tool that allows users to design PCR primers that are specific to their target sequence. Primer-BLAST uses the NCBI databases to identify the target sequence and design the PCR primers.
5.5 Conserved Domain Database
Conserved Domain Database is a database of protein domains and their function. Conserved Domain Database includes various tools, including CD-Search, which allows users to identify protein domains in their sequence.
5.6 COBALT
COBALT (Constraint-based Multiple Alignment Tool) is a tool that allows users to align multiple protein sequences based on their function and structure. COBALT is useful for identifying conserved domains and functional residues in protein sequences.
5.7 Cn3D
Cn3D (4D nucleotide and amino acid structure viewer) is a tool that allows users to visualize and analyze the 3D structure of nucleotide and protein sequences. Cn3D includes various tools, including sequence alignment and structure superposition.
6. NCBI Databases for Genomic Analysis
NCBI provides various databases that are useful for genomic analysis. Some of the most important NCBI databases for genomic analysis are discussed below.
6.1 Assembly
Assembly is a database of assembled genomes and their annotations. Assembly includes various tools, including genome comparison and gene annotation.
6.2 RefSeq
RefSeq is a database of reference sequences for various organisms, including humans, animals, plants, and microbes. RefSeq includes various tools, including gene annotation and functional analysis.
6.3 dbSNP
dbSNP (Single Nucleotide Polymorphism database) is a database of genetic variations, including SNPs (Single Nucleotide Polymorphisms), insertions, and deletions. dbSNP includes various tools, including SNP annotation and functional analysis.
6.4 GenBank
GenBank is a database of nucleotide sequences, including genomic and transcriptomic sequences. GenBank includes various tools, including sequence retrieval and annotation.
7. Conclusion
NCBI is a comprehensive resource for bioinformatics research, providing various databases, tools, and resources for genomic and sequence analysis. NCBI resources are free and easily accessible through the NCBI website, making it an essential tool for bioinformatics research.
FAQs
- What is NCBI? NCBI (National Center for Biotechnology Information) is a government-funded organization that provides various databases, tools, and resources for bioinformatics research.
- What are the major NCBI databases? The major NCBI databases include PubMed, GenBank, RefSeq, and dbSNP.
- What is BLAST? BLAST (Basic Local Alignment Search Tool) is a sequence similarity search tool that allows users to compare their sequences with the sequences in the NCBI databases.
- What is SRA? SRA (Sequence Read Archive) is a database of high-throughput sequencing data, including next-generation sequencing and third-generation sequencing data.
- How do I access NCBI resources? NCBI resources can be accessed through the NCBI website (https://www.ncbi.nlm.nih.gov/).