Date: ________________
Student’s name: __________________________________
Semester: ____________
Course name: Introduction to Bioinformatics (3(2,1))
Department: Computer Sciences
Course instructor: Dr. Maryam Mehmood
Lab 2
Title: How to retrieve protein sequences from Bioinformatics databases?
ExPASy: A prime internet site for protein information
Lab objectives:
Fundamental understanding of protein sequences information and their retrieval from known
protein sequences databases and web sources should be delivered to students through hands-on
training in Bioinformatics lab
Background information/introduction:
✓ What is ExPASy and how is it useful to retrieve protein information?
✓ What are other sources and databases to retrieve protein sequence information?
✓ What are related protein sequences and how do we retrieve them?
Lab requirements/Material required:
Computer systems, internet, lab manual and note book
Procedure:
1. Follow the given link to open NCBI Home Page: https://www.expasy.org/
2. Now, follow the given lab instructions to retrieve biological information from NCBI
3. After lab, submit your results (lab manual) to the lab instructor
Results:
i. Write down the purpose/function of the following SIB sources:
• Begee:
• STRING:
• SwissLipids:
• Cellosaurus:
• UniProt KB/Swiss-Prot:
1
• SWISS-MODEL:
• SWISS DrugDesign:
• Glyco@Expasy:
ii. Select one of the most useful and direct source to retrieve protein sequence information
from the given SIB sources:
iii. Protein name: ___________________________
iv. Search results: with a set of ____________ databases
v. Proteins and Proteomes (Report number of hits):
PROSITE ___________
STRING ____________
UniProtKB __________
ViralZone ___________
ENZYME ___________
UniProtKB
Total number of search hits:
Protein ID/Accession number:
Gene name/symbol:
Organism:
Chromosome#:
Number of amino acids:
PTMs:
Reviewed variants:
Isoforms:
Interactions:
Disease:
3D structures:
2
Reviewed publications:
Molecular function (#):
Protein Sequence (FASTA format):
Lab’s learning outcome/Conclusion/Inference:
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