BIOINFORMATICS

Chaitra.P.S – 3rd SEM, ML, SKIT,b’lore,csavkur@gmail.com

Namita.R-3rd SEM,ML,SKIT,b’lore,namnim_007@yahoo.co.in

1. ABSTRACT:

Bioinformatics is the application of computer technology to the management of

biological information. Computers are used to gather, store, analyze and integrate biological and
genetic information which can then be applied to gene-based drug discovery and development.
The science of Bioinformatics, which is the melding of molecular biology with computer
science, is essential to the use of genomic information in understanding human diseases and in
the identification of new molecular targets for drug discovery.

Development of this type of database involved not only design issues but the development
of complex interfaces whereby researchers could both access existing data as well as submit new
or revised data.
2.INTRODUCTION:

In order to study how normal cellular activities are altered in different disease states,
the biological data must be combined to form a comprehensive picture of these activities.
Therefore, the field of bioinformatics has evolved such that the most pressing task now involves
the analysis and interpretation of various types of data, including nucleotide and amino acid
sequences, protein domains, and protein structures. The actual process of analyzing and
interpreting data is referred to as computational biology. Important sub-disciplines within
bioinformatics and computational biology include: a)the development and implementation of
tools that enable efficient access to, and use and management of, various types of information
b)the development of new algorithms (mathematical formulas) and statistics with which to assess
relationships among members of large data sets, such as methods to locate a gene within a
sequence, predict protein structure and/or function, and cluster protein sequences into families of
related sequences. Bioinformatics is the application of information technology to the field of
molecular biology. Bioinformatics entails the creation and advancement of databases,
algorithms, computational and statistical techniques, and theory to solve formal and practical
problems arising from the management and analysis of biological data. Over the past few
decades rapid developments in genomic and other molecular research technologies combined
developments in information technologies have combined to produce a tremendous amount of
information related to molecular biology. It is the name given to these mathematical and
computing approaches used to glean understanding of biological processes. Common activities in
Bioinformatics include mapping and analyzing DNA and protein sequences, aligning different
DNA and protein sequences.

3. THEORY:

3.1. PROTEIN-BIOCHEMISTRY:

We are dealing with membrane proteins which are the key for many cellular processes.
One of the categories is structural bioinformatics where we deal with the protein structures. They
are primary, secondary, tertiary and quaternary structures. One of the main computational tasks
is protein structural alignment as given below and also we study about the DNA array.
3.2. What is an alignment?

A sequence alignment is a way of arranging the primary sequences of DNA, RNA, or

protein to identify regions of similarity that may be a consequence of functional, structural, or
evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino
acid residues are typically represented as rows within a matrix. Gaps are inserted between the
residues so that residues with identical or similar characters are aligned in successive columns.
When two symbolic representations of DNA or protein sequences are arranged next to
one another so that their most similar elements are juxtaposed they are said to be aligned. Many
bioinformatics tasks depend upon successful alignments. Alignments are conventionally shown
as traces.
In a symbolic sequence each base or residue monomer in each sequence is represented by
a letter. The convention is to print the single-letter codes for the constituent monomers in order
in a fixed font .This is based on the assumption that the combined monomers evenly spaced
along the single dimension of the molecule's primary structure.

3.3. Biological interpretation of an alignment

A trace can represent a substitution:
AKVAIL
AKIAIL
A trace can represent a deletion:
VCGMD
VCG-D

A trace can represent an insertion:

GS-K
GSGK

Traces may represent recent genetic changes which obscure older changes. Here we have only
represented point mutations for simplicity. Actual mutations often insert or delete several
residues.

3.4. What is DNA array?

DNA microarrays consist of thousands of immobilized DNA sequences present on a

miniaturized surface the size of a business card or less. Arrays are used to analyze a sample for
the presence of gene variations or mutations, or for patterns of gene expression.
DNA samples are prepared from the cells or tissues of interest. For genotyping analysis, the
sample is genomic DNA. For expression analysis, the sample is cDNA, DNA copies of RNA.
The DNA samples are tagged with a radioactive or fluorescent label and applied to the array.
Single stranded DNA will bind to a complementary strand of DNA. At positions on the array
where the immobilized DNA recognizes a complementary DNA in the sample, binding or
hybridization occurs. The labeled sample DNA marks the exact positions on the array where
binding occurs, allowing automatic detection. The output consists of a list of hybridization
events, indicating the presence or the relative abundance of specific DNA sequences that are
present in the sample.

4. CONCLUSION:

"Bioinformatics" is a rich field with many interesting problems.

 It is driven by money from the pharmas, who are driven, to some extent, by an aging
population and by advances in Science and Technology that allow things heretofore unattainable
to be done in the search for knowledge, drugs and diagnostics.

In protein biochemistry, DNA or protein sequences samples when subjected to

hybridization indicates the presence of specific DNA sequences and also helps in alignment.

5. REFERENCES:
1. Bond, P.J., Cuthbertson, J.M., Deol, S.S. and Sansom, M.S.P. (2004) MD simulations of
spontaneous membrane protein.

2. Deol, S.S., Bond, P.J., Domene, C. and Sansom, M.S.P. (2004) Lipid protein interactions of
integral membrane proteins.

3. Domene, C., Bond, P.J., Deol, S.S. and Sansom, M.S.P. (2003) Lipid protein interactions and
membrane/water interfacial region.

4. Campbell, J.D., Deol, S.S., Ashcroft, F.M., Kerr, I.D. and Sansom, M.S.P. (2004) Nucleotide
dependent conformational changes in HisP: molecular dynamics simulations of an ABC
transporter nucleotide binding domain.

5. Tai, K., Murdock, S., Wu, B., Ng, M.H., Johnston’s., Fangohr, H., Cox, S.J., Jeffreys, P.,
Essex, J.W. and Sansom, M.S.P. (2004) BioSimGrid: towards a world wide repository for
biomolecular simulations.