Course: Advance Bioinformatics and biostatistics

Q1: Briefly explain bioinformatics, history and its application

Q2: Explain gene and genome sequencing
Q3a. Differentiate Local and Global alignment
3b Differentiate Needleman and Wunsch algorithm & Smith Waterman algorithm.
Q4. Differentiate between PAM & BLOSSUM matrices
Q1:

Bioinformatics: A Definition

Bioinformatics involves the collection, comprehension, manipulation, classification, storage,

extraction, animation and usage of all biological information with the use of computer
technology. In modern biology, it is used to analyses and interpret data with the application of
tools.
History of Bioinformatics
The term first got recognition in the year 1970 by two scientists from the Netherlands, Paulien
Hogeweg and Ben Hesper. In their journals and records, we find bioinformatics as a study of
information processes in the biological world.
Application of Bioinformatics
We will now move on to the application of bioinformatics. Bioinformatics and its application
primarily lie in the extraction of useful facts and figures from a collection of data secured from
the natural world. Bioinformatics finds application in the fields of 3D image processing, 3D
modeling of living cells, image analysis, drug development, and a lot more. The most impactful
usage of bioinformatics is visible in the field of medicine, where we heavily employ its data to
create antidotes for infectious and harmful diseases.
The main application of bioinformatics is to make the comprehension of natural processes more
accessible and more uncomplicated.
Bioinformatics Applications List
Listed below are the various examples of the application of bioinformatics:
 We heavily employ bioinformatics in gene therapy.

 This branch finds application in evolutionary theory.

 Microbial analysis.
 Understanding of protein structure.
 Storage and revival of biotechnological data.
 In the discovery of new drugs.
 In agriculture to understand crop patterns, pest control, and crop management.
Uses of Bioinformatics
The uses of bioinformatics are plenty. We employ this science in data collection from the natural
world. We use it to develop technologies to understand our environment better. Bioinformatics
helps in the analysis of the very data that it gathers. Bioinformatics also helps in creating ways of
using this data to solve real-world problems. Therefore, this field is a very crucial part of
research and development. We can see its impact in a number of our industries and this aptly
highlights the importance and the extent of uses of bioinformatics.

Q2. Explain gene and genome sequencing

Sequencing genomes:

What is a Genome?

A genome is the complete set of genetic information of an organism. It contains all the
instructions for creating and maintaining life. Every living organism consists of a genome.

A human genome consists of nuclear and mitochondrial DNA. On the contrary, the genome of
a virus comprises RNA as the genetic material.

Our genome contains around 20,000 genes. They make up 1-5% of our genome. The DNA
between the genes is involved in gene regulation.

Genome Sequencing

The genome is a unique sequence of DNA. It is sequenced by certain machines to identify the
cause of a particular disease. Some diseases are caused by very little variation in the DNA.
Sequencing the genome can help us identify which DNA changes are causing the problem.

The genome of the tumour cells is altered when compared to normal cells. By comparing the
genome of the normal and cancer cells we can get clues about ways to treat cancer.

The sequencing of a human genome takes about a day. However, its analysis takes a longer time.

Applications of Genomics

Following are the important applications of genomics:

 Medical Applications

DNA and transgenes are used to create oral plant vaccines that stimulate immunity. Precision
medicine provides information about the genetic makeup of a patient to direct the type of
treatment they receive.

 Biotechnology Applications

Genomics has several applications in the field of bioengineering ad biotechnology. Mycoplasma

laboratorium was synthesised using the gene of Mycoplasma genitalium.
  Social Science

Genome sequencing is used in analysing the factors that are involved in the conservation of
species. For eg., the genetic diversity of a population can be used to predict the health and
conservation of species.

This helps in analysing the consequences of evolutionary processes and picking up genetic
patterns of a specific population. Analyses of these patterns can help to devise ways for the
conservation of species.

Q3a. Differentiate Local and Global alignment

3b Differentiate Needleman and Wunsch algorithm & Smith Waterman algorithm.

Needleman-Wunsch The Needleman-Wunsch algorithm , published in 1970, provides a method

of finding the optimal global alignment of two sequences by maximizing the number of amino
acid matches and minimizing the number of gaps necessary to align the two sequences. Because
the NeedlemanWunsch algorithm finds the optimal alignment of the entire sequence of both
proteins, it is a global alignment technique, and cannot be used to find local regions of high
similarity. In pairwise sequence alignment algorithms, a scoring function, F, must exist such that
different scores can be assigned to different alignments of two proteins relative to the number of
gaps and number of matches in the alignment. Thus, the alignment with the largest score must be
the optimal alignment. In this scoring function, let m be the score for two residues matching, s is
the penalty for mismatches, and g is the penalty for inserting a gap.

Smith-Waterman The Smith-Waterman algorithm was published in 1981 and is very similar to
the Needleman-Wunsch algorithm. Yet, the Smith-Waterman algorithm is different in that it is a
local sequence alignment algorithm. Instead of aligning the entire length of two protein
sequences, this algorithm finds the region of highest similarity between two proteins. This is
potentially more biologically relevant due to the fact that the ends of proteins tend to be less
highly conserved than the middle portions, leading to higher mutation, deletion, and insertion
rates at the ends of the protein. The Smith-Waterman algorithm allows us to align proteins more
accurately without having to align the ends of related protein which may be highly different. The
Smith-Waterman algorithm can be implemented by changing only a couple things in the
Needleman-Wunsch algorithm.

Q4:

PAM and BLOSUM matrices are used to score alignments between protein sequences, but they
differ in their applications. PAM matrices are used to score alignments between closely related
protein sequences, while BLOSUM matrices are used to score alignments between evolutionarily
divergent protein sequences1. PAM matrices are based on an explicit evolutionary model, while
BLOSUM matrices are based on an implicit model of evolution. PAM matrices are based on
mutations observed throughout a global alignment, while BLOSUM matrices are based on the
frequencies of amino acid substitutions in a database of aligned protein sequences