Databases used in Bioinformatics

The Databases (and their acronyms!):
 
Genbank, operated by NCBI (National Center for Biotechnology Information)
Contains all publicly available sequences of DNA, with annotations
Same DNA sequence content as EMBL (European Molecular Biology Laboratory) and DDBJ (DNA Data Bank of Japan)
Swiss-Prot and TrEMBL, operated by SIB (Swiss Institute of Bioinformatics) and EBI (European Bioinformatics Institute)
Contains most of the publicly available sequences of proteins, with annotations
Protein Data Bank
Contains all publicly availalble experimentally determined structural models of proteins and nucleic acids (determined by x-ray crystallography and NMR)
Swiss-Model Repository
Contains many theoretical structural models of proteins (determined by automated homology modeling)
Online Mendelian Inheritance in Man
A catalog of human genes and genetic disorders, linked to gene entries in GenBank

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How to use Genbank Database

The Genbank Sequence Database is an open access,annotated collection of all publically available sequences and their protein translations. This database is produced at NCBI as the part of INSDC .

For making use of Genbank follow this tutorial:
Making sense of the Genbank entry of the Prokaryotic Gene.
Go to:
www.ncbi.nlm.nih.gov/entrez/.
Select Nucleotide from search drop down menu and enter your query's accession number from Genbank. eg accession number is X01714 .The output page will be displayed which will tell you E.coli dut gene for dUTPase.
Then click the test button on the text bar to generate a true flat file format of the entry and you can save your entry
by choosing file save from your browser's main menu.
click on the hyperlink for further details of the entry.

the Genbank file format has three parts
1. Comment or defination line
2. Citation
3. Sequence
You can also view the Fasta format of the gene which includes the defination line and nucleotide sequence of your query.
from display settings select FASTA.
To go further retrieving Genbank  entries without using accession numbers.
 Select nucleotide from search drop down menu and type your query in the form of keywords as in the case of
 Human[organism] AND dUTPase [protein name].
Accession number search will give you the exact result of gene on locus but keyword search will give you many entries like exon 1,exon 2,exon 3, mRNA 1,mRNA 2 etc. different accession number entries indicate full amino acid sequence of the two forms of(nuclear and mitochondrial) of the dUTPase protein as well as alternative exon usage pattern.
 This tutorial will over I hope you will be benifited from this tutorial.
Regards "Quratt ul ain Siddique"

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What is Genbank Database

GenBank is the NIH genetic sequence database, an annotated collection
of all publicly available DNA sequences. GenBank (at NCBI), together
with the DNA DataBank of Japan (DDBJ) and the European Molecular
Biology Laboratory (EMBL) comprise the International Nucleotide
Sequence Database Collaboration. These three organizations exchange
data on a daily basis.

GenBank grows at an exponential rate, with the number of nucleotide
bases doubling approximately every 14 months. Currently, GenBank
contains more than 13 billion bases from over 100,000 species.

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