Introduction to NCBI

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Prerequisite Terminologies

In order to have thorough understanding of the main topic, you should have the basic concept of the following terms:

Primary Database.
Nucleotide, protein sequences.
LCT gene.

Duration: 

Transcription

By:

Hasnat Noor

Introduction:

The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is primary database, primary databases are archival in nature. They consist of experimentally derived data such as nucleotide sequence, protein sequence or macromolecular structure. Experimental results are submitted directly into the database by the researchers.

In this video we provide an introduction on NCBI. The NCBI is a host database, contains series of 32 sub-databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Each sort of database contains different data. This video consists step-wise information regarding the functionality of NCBI, 32 sub-databases of NCBI and an introductory sequence analysis on gene LCT.


Steps:

  • Homepage of NCBI contains hyperlinks to various sub-databases from which we can retrieve data of our interest and a query box to search.

  • There are total 32 sub-databases, such as include Biocollections, Assembly, Protein, Gene, Nucleotide, BioProject, OMIM, Books and various others.

  • In the query box type LCT, a key word for a gene that makes an enzyme Lactase.

  • Search it through all the databases.

  • Search result shows the reference of key word LCT in all databases. Mentions Homo sapiens as the most probable interest of search.

  • NCBI divides the search results in different categories of sub-databases.

  • Categories are Literature having books, articles, research papers in which LCT is mentioned, Gene providing genes from different organisms, Geo DataSets Geo profile for gene expression analysis, HomoloGene for homology analysis and PopSet for gene population analysis in set of organisms. Other categories Proteins for proteomics, Chemicals for finding substances compounds and their properties, Genetics for genotype-phenotype relationships, Genomes for genomic information.

  • From Gennome Genome category click on Nucleotide database showing a total of 7,856 nucleotide sequences of LCT gene in different organisms.

  • On the Nucleotide database search results page there’s list of 20 sequences out of 7,865 reference sequences of LCT gene on first page that can be extend up to 200 reference per page.


Summary:

NCBI is a public & primary database database of total 32 sub-databases, storing different datasets that are collected by researchers from all the world. In this video we discussed the functionality of NCBI and the search categories of NCBI. We performed an introductory sequence analysis on a gene called LCT and searched it through all the databases and found the references in different database and then moved to Nucleotide database from Genome category where we analysed the sequences of LCT gene.

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