KNIMT, Faculty of Pharmacy Notes: Computer Application in Pharmacy(BP205T)

Faridipur, Sultanpur

KNIMT, Faculty of Pharmacy

Faridipur, Sultanpur

NOTES
Computer Applications in Pharmacy
(BP205T)

Faculty Name: Vivek Srivastava

Faculty Name: Vivek Srivastava Page 1 of 6

 KNIMT, Faculty of Pharmacy Notes: Computer Application in Pharmacy(BP205T)
Faridipur, Sultanpur
BIOINFORMATICS(Unit IV)

Bioinformatics is an interdisciplinary field that develops methods and software tools for
understanding biological data, in particular when the data sets are large and complex. As an
interdisciplinary field of science, bioinformatics combines biology, computer science, information
engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics
has been used for in silico analyses of biological queries using mathematical and statistical
techniques.[clarification needed]
Bioinformatics includes biological studies that use computer programming as part of their
methodology, as well as a specific analysis "pipelines" that are repeatedly used, particularly in the
field of genomics. Common uses of bioinformatics include the identification of candidates genes
and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim of
better understanding the genetic basis of disease, unique adaptations, desirable properties (esp. in
agricultural species), or differences between populations. In a less formal way, bioinformatics also
tries to understand the organisational principles within nucleic acid and protein sequences, called
proteomics

OBJECTIVES OF BIOINFORMATICS
The field of bioinformatics has three main objectives:
1. 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. These data must be annoted to give a suitable meaning or to assign its
functional characteristics. The databases must also be able to correlate between different
hierarchies of information. For example: GenBank for nucleotide and protein sequence
information, Protein Data Bank for 3D macromolecular structures, etc.
2. 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, Primer3 to design primers probes for PCR
techniques, etc.
3. 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.

Faculty Name: Vivek Srivastava Page 2 of 6

 KNIMT, Faculty of Pharmacy Notes: Computer Application in Pharmacy(BP205T)
Faridipur, Sultanpur
LEVEL OF ORGANIZATION IN BIOINFORMATICS
Basically there are two sub-fields in bioinformatics:
1. Computational Bioinformatics
2. Application Bioinformatics

1. 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.

For example: A molecular biologist put forward the problems that he wants to get it solve. A
bioinformaticist analyzes the problem and suggests the possible way of handling the problem and
also bridges the gap between the biologist and computer experts. A computer scientist or a system
engineer designs a framework where the application can be built. Then the software engineer and
Mathematician/Statistician work together to design algorithm and ultimately cope up with an
application. And again the molecular biologist sits in the user end to evaluate if the software fulfills
his demands.

Database Construction and Curation: 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. There are countless public databases that
focus on different levels or types of biological information.

2. Application Bioinformatics:
All the applications of bioinformatics are carried out in the user level. Here is the biologist
including the students at various level can use certain applications and use the output in their
research or in study. Various bioinformatics application can be categorized under following
groups:
1. Sequence Analysis
2. Function Analysis
3. Structure Analysis

Faculty Name: Vivek Srivastava Page 3 of 6

 KNIMT, Faculty of Pharmacy Notes: Computer Application in Pharmacy(BP205T)
Faridipur, Sultanpur
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: These applications analyze the

function engraved within the sequences and helps predict
the functional interaction between various proteins or
genes. Also expressional analysis of various genes is a
prime topic for research these days.

Structure Analysis: When it comes to the realm of RNA and Proteins, its structure plays a vital
role in the interaction with any other thing. This gave birth to a whole new branch termed Structural
Bioinformatics with is devoted to predict the structure and possible roles of these structures of
Proteins or RNA

BIOINFORMATICS DATABASES

Databases are essential for bioinformatics research and applications. Many databases exist,
covering various information types: for example, DNA and protein sequences, molecular
structures, phenotypes and biodiversity. Databases may contain empirical data (obtained directly
from experiments), predicted data (obtained from analysis), or, most commonly, both. They may
be specific to a particular organism, pathway or molecule of interest. Alternatively, they can
incorporate data compiled from multiple other databases. These databases vary in their format,
access mechanism, and whether they are public or not.

Some of the most commonly used databases are listed below -

 Used in biological sequence analysis: Genbank, UniProt
 Used in structure analysis: Protein Data Bank (PDB)
 Used in finding Protein Families and Motif Finding: InterPro, Pfam
 Used for Next Generation Sequencing: Sequence Read Archive
 Used in Network Analysis: Metabolic Pathway Databases (KEGG, BioCyc), Interaction
Analysis Databases, Functional Networks
 Used in design of synthetic genetic circuits: GenoCAD

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 KNIMT, Faculty of Pharmacy Notes: Computer Application in Pharmacy(BP205T)
Faridipur, Sultanpur
IMPORTANCE OF BIOINFORMATICS
The field of computer science called bioinformatics is used to analyze whole-genome sequencing
data. This involves algorithm, pipeline and software development, and analysis, transfer and
storage/database development of genomics data.

A typical whole-genome sequencing workflow contains the following steps:

 quality control and data grooming;

 genome assembly and/or variant calling; and
 post-assembly analysis.

The volume of data that is produced from next-generation sequencing platforms is massive. Data
collected pertains not only to the DNA sequencing results but also on the sequencing performance
to assist with detection of errors or repetitive sequencing. This presents data management and
storage issues. Additionally, special software and fast computing systems are required to process
the immense data. Specialized, trained bioinformaticists are essential to the analysis of data
generated by next-generation sequencing, as well as the continued success and growth of precision
medicine.

Faculty Name: Vivek Srivastava Page 5 of 6

 KNIMT, Faculty of Pharmacy Notes: Computer Application in Pharmacy(BP205T)
Faridipur, Sultanpur

Faculty Name: Vivek Srivastava Page 6 of 6