Bc200203290
Department of Bioinformatics and Computational Biology
BIF401 – Bioinformatics – I
Assignment # 01 (Total Marks: 20) Fall 2021
Question # 1: Part (a) – (2.5 Marks)
Which types of issues/problems related to biological data are dealt with the “Bioinformatics”?
We all are well aware about bioinformatics that it have develop many software ,tools, databases and
online platform for the handling of huge biological data. That’s why bioinformatics help us in many ways
to resolve the problem that are related to biological data.
Biological data problems that are dealt with by bioinformatics are
Biological data storage
Major task in biology is the storage of data. Bioinformatics helps us to store huge amount of biological
date like nucleotide sequence data, protein sequence data, and protein structure etc.To store this huge
data that is increasing on daily basic bioinformatics use highly powerful computer for this purpose and
data base.
Biological data representation
In biological data representation data in the of graphics, chart, diagram and these are also a major issue
that is solved by the bioinformatics databases and software.
We use different software for this purpose like medusa, cityscapes etc.
To retrieval
Bioinformatics help us for the extraction of meaningful data form huge amount of data sets. To solve
this problems bioinformatics use different annotation tools to label the date sets with different tages.To
retrieve biological date different tools are used like entrez etc.
Data optimization
Drug discoveries, sequence etc.
Optimization is a major task. There is huge amount of possibilities for which correct and final result are
selected. Bioinformatics analyses not only accelerate drug candidates screening and refinement but also
help us in characterization of side effects and predict of drug resistance.
Analyzation of biological data
To analyze the complex biological data there are many difficulties. Bioinformatics tools made this very
easy. We can easily predict the three dimensional structure of protein that is very difficult. We can
analyze protein structure and function by Uniprot, swissprot etc.
Part (b) which alignment method is most suited to align closely related sequences? Explain in detail
There is two methods to align one is local aliment and second is global alignment. For closely related
sequence global aliment is perfect.
Global sequence alignment method is use to compare closely related to sequence. In this sequence we
can compares sequence end to end.
The most common technique for global alignment is Needleman wunsch alignment that ailing closely
related sequence.
Global alignment
Global alignment use to compare and ailing the entire sequence. Contains all letter for both query and
target sequence. Two sequences have quite same length and similar are suitable for global alignment.
Suitable for closely related sequence .use for compare homologous genes with same function.
Tool for global alignment
There are some techniques use to do global alignment.
I. EMBOSS Neede
II. Needleman wunsch Alignment
Dynamic programming approach consists of three steps.
Initialization
Matrix filling.
Trace back
Firstly we create matrix of M+I columns and N+I rows.
Initialization
Initially we fill the first row and column of matrix with zero.
Matrix filling
Now we calculate score for each cell by moving row by row we generally calculate their score and write
the minima score in each cell.
Match score
Vertical match
Horizontal gap score
Trace back
The last step is the trace back that’s starts for bottom right corner and we follow the path of minimum
score.
Question # 2: (10 Marks) Find the best global alignment, and its corresponding score between the
sequences, Sequence γ = CAATAC and Sequence β = TCGTC. Use a match score of 5, a mismatch score
of -5 and a gap penalty of -5. Show your work and fill the given Matrix
D T1 C2 G3 T4 C5
0 -5 -10 -15 -20 -25
C1 -5 -5 0 -5 -10 -15
A2 -10 -10 -5 -5 -10 -15
A3 -15 -15 -10 -10 -10 -15
T4 -20 -10 -15 -15 -5 -10
A5 -25 -15 -15 -20 -10 -10
C6 -30 -20 -10 -15 -15 -5
Mismatch=-5 Match score=5 Gap=-5
Global alignment
- C A A T A C
/ / / /
T C - G T - C
Score=-5
