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EBE 3202 Bioinformatics Practical & Competency Schedule

The document outlines the practical schedule for the Bioinformatics course (SBT 410) at the School of Industrial Sciences & Technology, detailing various experiments and competencies students are expected to achieve. It includes experiments related to DNA and protein data retrieval, biological data resources, sequence analysis, multiple sequence analysis, molecular phylogenetics, and genomics. Each experiment specifies the lab session and the skills students should develop through the practical work.

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16 views3 pages

EBE 3202 Bioinformatics Practical & Competency Schedule

The document outlines the practical schedule for the Bioinformatics course (SBT 410) at the School of Industrial Sciences & Technology, detailing various experiments and competencies students are expected to achieve. It includes experiments related to DNA and protein data retrieval, biological data resources, sequence analysis, multiple sequence analysis, molecular phylogenetics, and genomics. Each experiment specifies the lab session and the skills students should develop through the practical work.

Uploaded by

h220265n
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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School of Industrial Sciences & Technology

\ Department: Biotechnology
SBT 410 : Bioinformatics (SBT 410)
Lecturer : Mr. C. Mawere
Email ID : [email protected]

Practical Schedule
List of Experiments

Module Lab Name of the Experiment Lab Session Competencies


Exp.

1. Introduction to 1 DNA and/or protein data retrieval and LS1 Students should
Bioinformatics analysis in NCBI be able to search
the relevant
databases for
DNA or protein
information.

2 Protein data mining in Uniprot database LS1 Students should be


able to find the
protein function,
structural relevance
and annotation
studies.

2. Biological Data 3 Data mining of given protein ID in PDB LS2 Students should be
Resources database able to mine
release date,
resolution,
classification and
pub med citation of
the given protein
ID from PDB
Structure database.

4 Data mining of disease information from LS2 Students should be


KEGG database able to find the
disease pathway,
drug target
enzymes and drug
molecules used for
a given disease.

3. Sequence analysis 5 Pairwise sequence alignment for a given LS3 Students should
protein/DNA sequence by using Dot be able to align
matrix method Dothelix two DNA or

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protein sequences
and comment on
the results
inverted repeats,
palindromes.

6 Homolog sequence mining using BLAST LS3 Students are


expected to find the
homolog sequences
and study the
obtained output
using critical
statistical
parameters- the
%identity,
%similarity, P, and
E-values.

4. Multiple Sequence 7 Multiple sequence analysis using the LS4 Students should be
analysis ClustalW/T-coffee able to find the
multiple sequence
alignment using the
ClustalW/T-coffee
and find the
conserved regions,
motifs and profiles.

8 Homology modelling of protein 3D LS4 Students should be


structures able to predict a 3D
protein structure
model for a given
protein sequence
by using the Swiss
modeler online
tool.

9 Phylogenetic tree construction using LS5 Students should be


distance based methods able to find
Distance-Based
5. Molecular Phylogenetic Tree
Phylogenetics for a given protein
sequence and find
the length of the
root node using
MEGA tool.

10 Phylogenetic tree construction using LS5 Students must be


character based methods able to generate a
Maximum
Likelihood Tree
Using Genetic
Algorithm for a
given protein

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sequence using
PHYML web page.

6. Genomics 11 Gene prediction in eukaryotes LS6 Students should be


able to predict the
promoter for a
given DNA
sequence by using
the Genmark
/Genscan/Genlang
and analyse the
results.

12 Gene prediction in prokaryotes LS6 Students should be


able to identify and
locate the promoter
and repressor for a
given DNA
sequence by using
BPROM/SAK.

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