Bio Informatics (AL-803 (B)) - Important Questions
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Unit 214 Marks High Priority
Describe the main types of bioinformatics databases (nucleotide sequence databases, protein sequence databases, and protein structure databases) and explain how they are organized and accessed by researchers.
Core, frequently asked broad question covering all major database types in Unit 2 (nucleotide, protein sequence, protein structure). High-value for exam preparation.
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Unit 27 Marks High Priority
Explain nucleotide sequence databases. Include major examples (e.g., GenBank, EMBL, DDBJ), how records are organized (accession numbers, annotations), and common search and retrieval tools.
Direct focus on nucleotide sequence databases — a recurring Unit 2 topic. Targets examples, organization and search/access methods.
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Unit 27 Marks High Priority
Explain protein sequence databases. Discuss major resources (e.g., UniProt/Swiss-Prot, TrEMBL, PIR), their organization, annotation types, and the difference between manually curated and automatically annotated entries.
Direct focus on protein sequence databases — a recurring Unit 2 topic. Emphasises differences between curated and automated resources.
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Unit 27 Marks Medium Priority
What are protein structure databases? Explain the Protein Data Bank (PDB), common structure classification resources (e.g., SCOP, CATH), data formats used, and how structural data are retrieved and visualized.
Covers the protein structure database topic that appears repeatedly in Unit 2 past items; focuses on PDB and classification resources.
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Unit 214 Marks Medium Priority
Explain methods for pairwise sequence alignment. Compare dynamic programming approaches (Needleman–Wunsch, Smith–Waterman) with heuristic approaches (e.g., BLAST, FASTA), and discuss advantages and disadvantages of each.
Standard comparison question for sequence alignment approaches: dynamic programming vs heuristics (common exam pattern).
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Unit 210 Marks Low Priority
Describe a computational pipeline for protein structure prediction. Outline the main approaches (homology modelling, fold recognition/threading, ab initio), the key stages in a modelling workflow, and the challenges encountered at each stage.
Important predictive question on structure prediction pipelines; tests understanding of methods and challenges at each stage.
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Unit 210 Marks Low Priority
Explain gene finding strategies. Compare ab initio methods with evidence-based (homology, transcript alignment) approaches and list commonly used gene prediction tools and the features they exploit.
Predictive but important topic in bioinformatics: gene finding strategies are central to sequence analysis and often examined.
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Unit 27 Marks Low Priority
Outline strategies for mining gene expression data. Describe key preprocessing steps (normalization, quality control), common clustering and dimensionality‑reduction techniques, and approaches to identify differentially expressed genes.
Covers analysis of high-throughput expression data — a common applied bioinformatics question. Useful for practical and theory exams.
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Unit 210 Marks Medium Priority
Describe methods for searching sequence databases. Explain BLAST family tools (blastn, blastp, blastx), the role of scoring matrices (PAM, BLOSUM), and how e-values are used to assess match significance.
Covers sequence search methods and scoring concepts that are fundamental when working with sequence databases.
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Unit 27 Marks Medium Priority
Compare common sequence file formats used in bioinformatics (FASTA, FASTQ, GenBank). Explain the key differences, typical uses, and the type of information contained in each format.
Practical question on common file formats used in sequence databases; regularly required knowledge for database handling and pipelines.
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