Bio-Informatics, Its Application S& Ncbi: Submitted By: Sidhant Oberoi (BTF/09/4038)

Bio-
informatics
Submitted by:
, its Sidhant Oberoi
application (BTF/09/4038)
s&
NCBI
The assignment contains a brief introduction about
bioinformatics and its applications. It also focuses on
National Centre for Biotechnology Information, its origin,
working and objectives.
Introduction to Bio Informatics
The term bioinformatics was coined by Paulin Hogeweg in 1979 for the study
of informatics process in biotic systems. Recent development in technologies
and instrumentation, which allow large scale as well as nano scale probing of
biological samples, are generating an unprecedented amount of digital data.
This sea of data is too much for the human brain to process and thus there is an
increasing need to use computational methods to process and contextualise
these data.
Bioinformatics refers to the study of biological information using concepts and

methods in computer science, statistics, and engineering. It can be divided into
two categories: biological information management and computational biology.
National Institute of Health defines the former category as “research,
development, or application of computational tools and approaches for
expanding the use of biological, medical behavioural or health data including
those to acquire, represent, describe, store, analyse, or visualise such data”. The
later category is defined as, “the development and application of data analytical
and theoretical method, mathematical modelling, and computational simulation
techniques to the study of biological, behavioural, and social systems”. The
boundaries of these categories are becoming more diffuse and other categories
will no doubt surface in future as this field matures. Over past few decades
rapid development in genomics and other molecular research technologies and
development in information technologies have combined to produce a
tremendous amount of information related to molecular biology. Common
activities in bioinformatics include mapping and analysing DNA and protein
sequences, aligning different DNA and protein sequences to compare them and
creating and viewing 3D models of protein structures. The primary goal of
bioinformatics is to increase the understanding of biological processes at an
ease by using the computational technology.
Applications of Bioinformatics:
In today’s date bioinformatics is being used in the fields like Molecular

medicine, Preventative medicine, Personalised medicine, Gene therapy, Drug
Development, Microbial Genome applications, Waste cleanup, Climate change
studies, Alternative energy sources, Biotechnology, Antibiotic resistance,
Forensic analysis of microbes, Bio-weapon creation, Evolutionary studies, Crop
improvement, Insect resistance, Improving nutritional quality, Development of
drought resistant varieties, Vetinary science. These are the diverse field where
the benefit of bioinformatics is being taken. Applications of bioinformatics have
been helping to bridge the gap between what was once thought of as a far off
possibility and a near reality in the study of human genome and the comparison
of genetic information in other species. When it comes to the different
applications of bioinformatics, the options are limitless. There are constantly
being new research projects and studies being done on this amazing new line of
DNA analysis. Scientists are now using bioinformatics to detect genetic
abnormalities in different species. This is also creating breakthroughs in the
medical community. Applications of bioinformatics have allowed doctors to
conduct genetic testing in unborn babies to predict and find any signs of certain
genetic disorders and conditions.
http://www.ncbi.nlm.nih.gov
This is the official web page of National Centre for Biotechnology
Information
NCBI:
National Centre for Biotechnology Information
NCBI is called as the database of different databases, as it provides information

about different biological data which is stored in different databases. There are
several databases which are linked with NCBI and provide information to it.
NCBI was created by the Public Law 100-607 in 1988 as a part of National
Library of Medicine at NIH (National Institute of Health, which is one of the
oldest research institute of Department of Health & Human Services, United
States). NCBI is located in Bethesda, Maryland. It is now directed by David
Lipman, one of the original authors of the BLAST sequence alignment
programme.
One of the most difficult challenges faced in the field of bioinformatics is how
to store, in an easily accessible manner, the overwhelming abundance of new
information, including the sequences of all genomes, the ongoing discoveries of
new genes and gene products, and the determination of their functions and
structures. The major aim of NCBI is to create automated systems for
knowledge about the diverse branches of biology like molecular biology,
biochemistry, microbiology, genetics etc. It aims at helping the researchers to
perform research into advanced methods of analysing and interpreting
biological data. It simply acts as the best central library for all the biotechnology
researchers, professionals or students. It is the major centre for the basic
research and training in computational biology.
NCBI also provides Entrez databases. Entrez is the integrated, text based search
and retrival system used at NCBI for the major databases, including PubMed,
Nucleotide and Protien sequences,
protein Structures, Complete
Genomes, Taxonomy, and others. The
complete list of Entrez databasesis
shown as follows:
NUCLEOTIDE DATABASES:
dbEST, dbGSS, dbSNP, dbSTS,

Nucleotide, GenBank, HomoloGene,
MGC, PopSet, Probe, RefSeq, Entrez: Pathway to Discovery
SRA, TPA, TraceArchive,
UniGene, UniSTS.
PROTIEN DATABASES:
3D Domains, Protiens, Protien Clusters, PROW, RefSeq.
STRUCTURE DATABASES:
Conserved Domains, 3D Domains, Structure (MMDB).
TAXONOMY DATABASES:
Taxonomy.
GENOME DATABASES:
Cancer Chromosomes, COGs, Gene, Genome Project, Genomes.
EXPRESSION DATABASES:
GEO Profiles, GEO Datasets.
CHEMICAL DATABASES:
PubChemBioAssay, PubChemSubstance, PubChemCompound.

NCBI contains several databases of Literature, taxonomy, genomes, sequences
etc. It allows the user to select the database of its field of interest. The user can
select a particular database or can select the type of information he wants, like
protein, structure, books, journals etc. If we talk about the NCBI gene database,
it provides highly summarized information about the genes for all the species
where it is available. It helps in understanding the genomic structures and
transcripts of a gene, obtaining marker information, obtaining information about
the function of the gene products and identifying related sequences and
conserved domains. The database of gene basically contains alternative gene
identifiers, gene structures and genomic information, genetic markers,
phenotypes, sequences and mapping data, including physical maps. NCBI is
today’s most heavily visited website in biomedicine. The statistics say that
NCBI experiences 722,000 Unique IP’s a day, 1.8 Million Unique users a day,
91 million web hits a day, 3200 Peak web hits a second and 1.5 Terabytes FTP a
day.
NCBI is today considered the best source of knowledge for the field of
biotechnology. It also allows the user for the retrieval of data in various formats
as per the requirement of the user, like GenPept, FASTA, FASTA text etc.
NCBI also has a FTP site with the URL: (ftp.ncbi.nih.gov). The major resources
under the FTP site are BLAST, CDD data, CD-Tree, Cn3D, dbGap, Genebank
etc. NCBI makes its users available with various research papers in different
topics. Most of them are available free of cost while some are available after the
payment of the membership fee. The database of NCBI is updated every week,
on Tuesday evening and the latest update is available to the user on Wednesday.
Let us take an example, if a user wants to retrieve some information about any
particular protein, say ‘human insulin’. Then the user will need to enter the
name of the protein in the search column, human insulin in this case and should
select the proper database. ‘Protein’ will be an appropriate database in this case.
After selecting all these columns, clicking on the search option will provide
with the list of all the available results. When this example was checked, it
provided me 4938 results. Then it also gives the option of the format required,
for example GenPept, FASTA etc. Finally the user can obtain the desired result
in the desired format.
In short we can say that National Centre for Biotechnology Information

advances science and health by providing access to biomedical and genomic
information.

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Bio-

Bioinformatics refers to the study of biological information using concepts and

In today’s date bioinformatics is being used in the fields like Molecular

NCBI is called as the database of different databases, as it provides information

dbEST, dbGSS, dbSNP, dbSTS,

3D Domains, Protiens, Protien Clusters, PROW, RefSeq.

Conserved Domains, 3D Domains, Structure (MMDB).

Cancer Chromosomes, COGs, Gene, Genome Project, Genomes.

GEO Profiles, GEO Datasets.

PubChemBioAssay, PubChemSubstance, PubChemCompound.

In short we can say that National Centre for Biotechnology Information

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