basics of bio informatics

1. BIOINFORMATICS:
Basic concepts
Presented by
Ratul Nath
(Former INSPIRE Fellow)
Assistant Professor
B. N. College, Dhubri

2. What is Bioinformatics?

3. An emerging discipline of Biotechnology which has now
become the heart of modern biological research.
Bioinformatics, was coined by Paulien Hogeweg, by
combining– Biology and Information Technology (IT).
Bioinformatics is the systematic development and application of
IT solutions to handle biological information by addressing
biological data collection and warehousing, data mining, database
searches, analyzes and interpretation, modeling and product
design.

4. The field of science in which biology, computer science
and information technology merge into a single discipline .

5. BRANCHES OF BIOINFORMATICS
Computational
Bioinformatics
Structural
bioinformatics
Application
bioinformatics

6. Computational Bioinformatics

7. Application bioinformatics

8. Computational Bioinformatics
It refers to all the computational work done so as to develop
an application that is aimed to address certain problems in biology.
Computational Bioinformatics further has the following levels:
Algorithm and Software Development:
To solve any problem we first must have a strategy
to tackle the problem For this algorithm of the
application is a must. Here people with different
expertise work together to develop an algorithm.

9. A molecular biologist put forward the problems
A bioinformaticist suggests the possible way of
handling the problem
A computer scientist or a system engineer designs
a framework
Software engineer and Mathematician/Statistician
design algorithm
Molecular biologist sits in the user end to evaluate
if the software fulfills his demands
How to develop an algorithm

10.  Any information generated in the lab must be stored
in a database for easy retrieval in the future.
 Without database bioinformatics becomes lame.
 Database is a place where one can store related
information which makes the information much more
meaningful and help in the future development.
Database Construction and Curation:

11. APPLICATION BIOINFORMATICS:
This part of bioinformatics is directly related to users
including students as well as researchers. From this part output of
bioinformatics is obtained. Various bioinformatics application can
be categorized under following groups:
Sequence analysis
Functional analysis
Structural analysis

12. Sequence Analysis:
All the applications that analyzes various types of
sequence information and can compare between similar
types of information is grouped under Sequence
Analysis.
Function Analysis:
It mainly deals with functions of genes and their
products i.e. proteins.
Analysis Structure:
Structural Bioinformatics which is devoted to predict the
structure and possible roles of these structures of Proteins or
RNA.

13. AIMS OF BIOINFORMATICS
In general, there are three basic aims of bioinformatics…
The first aim of bioinformatics is to store the
biological data organized in form of a database. This
allows the researchers an easy access to existing
information and submit new entries.

14. The second aim is to develop tools and resources that aid
in the analysis of data. For example: BLAST to find out
similar nucleotide/amino-acid sequences, ClustalW to
align two or more nucleotide/amino-acid sequences.
The third and the most important aim of
bioinformatics is to exploit these computational tools to
analyze the biological data interpret the results in a
biologically meaningful manner.

15. RSEARCH AREAS OF BIOINFORMATICS
.
In experimental molecular biology
In Genetics and genomics, it aids in sequencing and
annotating genomes and their observed mutations
Textual mining of biological literature
Analysis of gene and protein expression and regulation
Understanding of evolutionary aspects of molecular
biology
Analyze and catalogue the biological pathways and
networks that are an important part of systems biology.

17. BIOLOGICAL DATABASE
Biological databases are libraries of life sciences information,
collected from scientific experiments, published literature, high-
throughput experiment technology, and computational analyses.
They contain information from research areas including genomics,
proteomics, metabolomics, microarray gene expression, and
phylogenetics.

19. Types of Biological Databases With Respect To
Information They Contain

20. Types of Biological Databases With
Respect To Their Nature

24. Types of Biological Databases According To
Their Function
Primary nucleotide sequence databases
The International Nucleotide Sequence Database (INSD)
consists of the following databases.
DNA Data Bank of Japan (National Institute of Genetics)
European Nucleotide Archive (European Bioinformatics
Institute)
GenBank (National Center for Biotechnology Information)
The three databases, are repositories for nucleotide sequence
data from all organisms.

25. Genome databases
These databases collect organism genome sequences,
annotate and analyze them, and provide public access.. These
databases may hold many species genomes, or a single model
organism genome.
Bioinformatic Harvester
SNPedia
CAMERA Resource for microbial genomics and metagenomics
Corn, the Maize Genetics and Genomics Database
EcoCyc a database that describes the genome and the biochemical
machinery of the model organism E. coli K-12

26.  Protein sequence databases
UniProt: Universal Protein Resource (EBI, Swiss Institute of
Bioinformatics, PIR)
Swiss-Prot: Protein Knowledgebase (Swiss Institute of
Bioinformatics)
PROSITE: Database of Protein Families and Domains
Database of Interacting Proteins (Univ. of California)
Pfam: Protein families database of alignments and HMMs
(Sanger Institute)

27. Proteomics databases
Proteomics Identifications Database (PRIDE) A public
repository for proteomics data.. (European Bioinformatics Institute)
MitoMiner - A mitochondrial proteomics database (MRC
Mitochondrial Biology Unit)
GelMap - A public database of proteins identified on 2D gels
(University of Hanover Proteomics Department)

28. Protein structure databases
Protein Data Bank (PDB) comprising:
Protein DataBank in Europe (PDBe)
ProteinDatabank in Japan (PDBj)
(RCSB) Research Collaboratory for Structural
Bioinformatics

29. RNA databases
Rfam, a database of RNA families
miRBase , the microRNA database
snoRNAdb, a database of snoRNAs

30. Biological database
retrieval systems

31. How to Perform Database-Searching
As the amount of biological relevant data is
increasing so rapidly, it is essential to know how to
access and search information on them. There are
three data retrieval systems to molecular biologist:
Sequence Retrieval System (SRS), Entrez, and
DBGET.

32. SRS is a homogeneous interface to over 80
biological databases that had been developed at the
European Bioinformatics Institute (EBI) at Hinxton, UK.
It includes databases of sequences, metabolic
pathways, transcription factors, application results (like
BLAST, SSEARCH, FASTA), protein 3-D structures,
genomes, mappings, mutations, and locus specific
mutations.
Sequence Retrieval System (SRS)

34. Database Description
PubMed The biomedical literature
Nucleotide Sequence database (genbank0
Protein Sequence database
Structure 3 D macromolecular structures
Genome Complete genome assemblies
PopSet Population study
OMIM On line Mendelian inheritance in man
Taxonomy Organisms in genbank
SNP Single nucleotide polymorphism
Conserved domains CDD

35. DBGET
DBGET is an integrated database retrieval
system, developed at the university of Tokyo.
Provided access to 20 databases, one at a time.
Having more limited options, the DBGET is less
recommended than the two others.