Bioinformatics and NGS Sequence Analysis Portal 02
Bioinformatics and NGS Sequence Analysis
Internship Task Portal – 02 | Study Material & Practical Assignments
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Welcome to Internship Task Portal – 02
This portal contains the next set of learning activities for the Bioinformatics and NGS Sequence Analysis Internship.
Unlike the previous portal, these tasks are provided in a study-material format. Interns are expected to read the learning material, perform the suggested practical/research activities and submit their assignments.
Important: Complete the tasks in sequence and maintain screenshots, notes and reports wherever requested.
🧬 Bioinformatics and NGS Sequence Analysis – Portal 02 Update
Portal 02 focuses on important concepts used after understanding basic NGS data and quality control. The activities introduce interns to sequence databases, sequence alignment, genome annotation concepts and biological data interpretation.
During this portal, you will:
- Understand biological sequence databases.
- Learn how to search and retrieve biological sequence information.
- Understand sequence alignment and similarity analysis.
- Explore BLAST and its applications in bioinformatics.
- Understand genome annotation and gene prediction concepts.
- Study basic interpretation of genomic analysis results.
- Prepare research-based assignments and practical reports.
No video session is required for these tasks at this stage. Use the study points, recommended resources, practical instructions and research activities provided inside each task.
TASK 1: Biological Sequence Databases & NCBI Resources
Understand the purpose of biological databases and learn how resources such as NCBI can be used to search, retrieve and study biological sequence information.
Topics to Study
- What are biological databases?
- Primary vs secondary biological databases.
- Introduction to NCBI.
- NCBI Nucleotide database.
- NCBI Protein database.
- GenBank and RefSeq.
- NCBI Gene database.
- NCBI Genome resources.
- Accession numbers and why they are important.
- FASTA sequence retrieval.
- Visit the NCBI website.
- Search for a gene of your choice.
- Record the gene name and organism.
- Find its NCBI Gene entry.
- Identify at least one accession number.
- Retrieve a FASTA sequence related to your selected gene.
- Take screenshots of your search and retrieved sequence.
“Importance of Biological Databases in Modern Bioinformatics Research”
Include examples of NCBI, GenBank, RefSeq and protein/sequence databases.
- Study notes
- Assignment report
- Selected gene name
- Accession number
- NCBI screenshots
- FASTA sequence screenshot
📂 Task Submission
After completing the task, submit your work through the Internship Task Completion Form.
Submit Task 1TASK 2: BLAST – Sequence Similarity Search
Understand the basic concept of sequence similarity searching and learn how BLAST can be used to compare biological sequences with existing database sequences.
Topics to Study
- What is sequence similarity?
- What is BLAST?
- Basic principle of BLAST.
- BLASTN vs BLASTP.
- Query sequence and subject sequence.
- Understanding percentage identity.
- Understanding query coverage.
- Understanding E-value.
- Understanding alignment score.
- Biological interpretation of BLAST results.
- Obtain a short nucleotide or protein sequence from NCBI.
- Open the appropriate NCBI BLAST tool.
- Enter the sequence as a query.
- Run the similarity search.
- Observe the top matching sequences.
- Record the top hit.
- Record percentage identity.
- Record query coverage and E-value.
- Take a screenshot of the BLAST result.
Prepare a small table containing:
- Top hit
- Organism
- Percentage identity
- Query coverage
- E-value
- Accession number
Write a 250–350 word report titled:
“Understanding BLAST and Its Importance in Sequence Analysis”
- Study notes
- BLAST screenshot
- Top hit information
- Result interpretation table
- Assignment report
📂 Task Submission
Submit Task 2TASK 3: Genome Annotation & Gene Prediction Concepts
Understand the basic principles of genome annotation and how computational methods are used to identify genes and functional elements in genomic sequences.
Topics to Study
- What is genome annotation?
- Structural vs functional annotation.
- What is a gene?
- Open Reading Frames (ORFs).
- Promoters and regulatory regions.
- Exons and introns.
- Gene prediction.
- Reference genomes.
- Functional annotation.
- Gene Ontology (GO) concepts.
- Importance of genome annotation in research.
- Select one well-studied organism.
- Research how its genome is annotated.
- Identify at least three genes from the organism.
- Record the gene names and their known functions.
- Identify whether the genes code for proteins.
- Research one example of a gene annotation database.
Create a simple diagram showing the relationship:
DNA → Gene → Transcript → Protein → Biological Function
Explain each stage in your own words.
Write a 300–400 word report:
“Role of Genome Annotation in Understanding Gene Function”
- Study notes
- Genome annotation research
- Three selected genes
- Gene-function information
- DNA → Gene → Protein diagram
- Assignment report
📂 Task Submission
Submit Task 3TASK 4: Mini NGS Data Interpretation & Bioinformatics Report
Combine the concepts learned during the internship and prepare a simple bioinformatics interpretation report using an NGS analysis workflow.
Review These Concepts
- NGS data generation.
- FASTQ files.
- Sequence quality scores.
- FastQC quality assessment.
- Quality trimming.
- Sequence alignment.
- Reference genomes.
- BLAST and sequence similarity.
- Genome annotation.
- Biological interpretation of computational results.
Prepare a simplified NGS analysis workflow based on the concepts learned so far.
Raw FASTQ Data
↓
Quality Control
↓
Read Preprocessing
↓
Sequence Alignment
↓
Result Analysis
↓
Annotation / Biological Interpretation
- Select one publicly available NGS dataset or published NGS study.
- Record the study title.
- Identify the organism used.
- Identify the type of sequencing data.
- Identify the approximate purpose of the study.
- Find out which bioinformatics tools were used, if reported.
- Summarize the analysis workflow.
Create a table similar to the following:
| Stage | Purpose | Example Tool |
|---|---|---|
| Quality Control | Check raw reads | FastQC |
| Preprocessing | Improve read quality | Trimming tools |
| Alignment | Map reads | Alignment software |
| Annotation | Interpret genes/features | Annotation databases |
Prepare a 500–700 word mini-report titled:
“Bioinformatics Workflow for NGS Data Analysis: From Raw Sequencing Reads to Biological Interpretation”
Your report should contain:
- Introduction
- NGS data description
- Quality control
- Preprocessing
- Alignment
- Annotation
- Biological interpretation
- Conclusion
- Study notes
- NGS study/dataset information
- Analysis workflow diagram
- Final analysis table
- Mini-project report
- Relevant screenshots/references
📂 Task Submission
Upload your completed work through the official internship submission form.
Submit Task 4📊 Portal 02 Completion Checklist
- Complete all four tasks independently.
- Use your own words while preparing reports and notes.
- Do not submit copied assignments from online sources.
- Keep screenshots of practical/research activities.
- Use the official submission form for task completion.
- Make sure the submitted files are readable and properly named.
- If you face difficulty with any task, contact your internship mentor/team.
Please make sure your attendance is marked before/after participating in the scheduled internship activity.
👉 Mark Your Attendance⏱ Estimated completion time: 5 working days per portal.