Genomic Databases

1. GENOMIC
DATABASES
KATTULA JYOSTHSNA

2. Introduction:
• Gene: functional unit controlled by transcription that
produces a RNA product, which is most frequently but not
always translated into a protein that acts inside or outside of
a cell.
• Genome: the complete set of genes and genetic material
present in an organism.
• Genomic: Entire genetic information of an organism, the
genome and the function and interaction of DNA within the
genome.

3. What is a Genomic Database?
The Genome Database (GDB, http://www.gdb.org ) is a public repository of data on human genes, clones,
STSs, polymorphisms and maps. GDB entries are highly cross-linked to each other, to literature citations and
to entries in other databases, including the sequence databases, OMIM, and the Mouse Genome Database.
The database can be searched by a variety of methods, ranging from keyword searches to complex queries
The content of GDB comes primarily from two sources: the scientific literature and submission from data
producers

4. • The 3 main nucleic acid databases:
• DNA Data Bank of Japan (National Institute of Genetics)
• EMBL (European Bioinformatics Institute)
• GenBank (National Center for Biotechnology Information)
• NCBI GenBank, EMBL Nucleotide Sequence Database (EMBL), and the DNA Data Bank of Japan
(DDBJ) are comprehensive databases that contain publicly available nucleotide sequences. The three
organizations synchronize their data on a daily basis to ensure worldwide coverage.
• GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA
sequences GenBank is part of the International Nucleotide Sequence Database Collaboration, which
comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and
GenBank at NCBI. These three organizations exchange data on a daily basis.
• FASTA - a text-based format for representing either
nucleotide sequences or peptide sequences,
in which base pairs or amino acids are represented using
single-letter codes. A sequence in FASTA format begins with
a single-line description, followed by lines of sequence data.

5. Access to GenBank
There are several ways to search and retrieve data from GenBank.
Search GenBank for sequence identifiers and annotations with Entrez Nucleotide.
Search and align GenBank sequences to a query sequence using BLAST (Basic Local Alignment
Search Tool). See BLAST info for more information about the numerous BLAST databases.
Search, link, and download sequences programatically using NCBI e-utilities.
The ASN.1 and flatfile formats are available at NCBI's anonymous FTP
server: ftp://ftp.ncbi.nlm.nih.gov/ncbi-asn1 and ftp://ftp.ncbi.nlm.nih.gov/genbank.

6. Methods of retrieving
information:
• Querying by name, keyword or
accession number
• Querying by region of interest.
• Retrieving a graphical view of
locus position
Querying by name, keyword or accession
number:
• The simplest search methods available are:
• find an object with a known GDB accession
number
• find objects associated with a known sequence
database accession number
• find objects having a specified name. The name
can include wildcard symbols (e.g., AFM147×b*),
and will automatically match synonyms as well as
primary names.
• find objects that contain one or more keywords
anywhere in their text.

7. Types of Genomic databases
Entrez_Genomes; EBI_Genomes : Databases that
collect data of all sequenced genomes
Microbial Genome at TIGR : Databaes that collect data
of a category of organism with sequenced genomes
Flybase, MGD, Ensembl : Databases specific for one
organism with sequenced genomes.

8. Flybase - a database of the Drosophila genome
GenProtEC - E.Coli genome and proteome database
GOBASE - the organelle Genome Database
Gramene – a resource for comparative grass genomics
HGD – Hymenopetra Genome Database
IGGI – International Glossina Genome Initiative
PomBase – a scientific resource for fission yeast

9. Resources:
• https://www.ncbi.nlm.nih.gov/genome/
• https://www.researchgate.net/publication/22
7990866_Genome_Databases
• https://www.ncbi.nlm.nih.gov/genbank/
• https://www.ncbi.nlm.nih.gov/Class/MLAC
ourse/Modules/Databases/databases_scope.
html#:~:text=Human%20Genome%20Sequ
encing,SGD%3A%20Saccharomyces%20G
enome%20Database