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Information retrieval from databases - search concepts, Tools for searching, homology searching, finding Domain and Functional site homologies Information Retrieval from Databases 1. Introduction Information retrieval in bioinformatics refers to the process of extracting relevant biological data (DNA, RNA, protein sequences, structures, or functional information) from databases. Aim : Identify sequences, functions, or structural features for analysis, comparison, and annotation. Databases can be primary (raw sequence data) or secondary/derived (annotated, processed data). 2. Search Concepts in Biological Databases 2.1 Types of Searches Exact Match Search Returns results only if the query exactly matches database entries. Useful for known accession numbers or IDs. Pattern/Keyword Search Searches based on specific motifs, keywords, or annotations. Example: “kinase domain,” “signal peptide.” Similarity/Homology Search Detects sequences similar to the query based on sequence alignment. Use...

Protein Structure Database (PDB) Introduction The Protein Structure Database (PDB) is the primary global repository for the three-dimensional (3D) structures of biological macromolecules such as proteins, nucleic acids, and protein–ligand complexes. These structures are determined experimentally using techniques like X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and Cryo-Electron Microscopy (Cryo-EM). PDB plays a vital role in understanding: Protein structure and function Molecular interactions Drug discovery and design Structural biology and bioinformatics History and Development Established in 1971 Founded by Brookhaven National Laboratory (USA) Initially contained only 7 protein structures Now maintained by the Worldwide Protein Data Bank (wwPDB) Members of wwPDB RCSB PDB (USA) PDBe (Europe) PDBj (Japan) BMRB (Biological Magnetic Resonance Data Bank) Objectives of PDB To collect, store, and distribute 3D structural data of biomolecules To provide free and ope...

Secondary Databases (PROSITE, PRINTS, BLOCKS  Secondary Databases Introduction Biological databases are broadly classified into primary and secondary databases. Primary databases store raw experimental data (e.g., nucleotide or protein sequences), whereas secondary databases contain derived information obtained by analyzing primary sequence data. Secondary databases are mainly used to: Identify protein families Detect conserved motifs, patterns, and domains Predict protein function Study structure–function relationships Examples of secondary databases include PROSITE, PRINTS, BLOCKS, Pfam, etc. 1. PROSITE Database Definition PROSITE is a secondary database that documents protein domains, families, and functional sites in the form of patterns and profiles. Developed by Swiss Institute of Bioinformatics (SIB) Maintained along with UniProt Principle PROSITE is based on the idea that functionally important regions of proteins are conserved during evolution. These conserved regions can ...

Protein Sequence Databases PIR, SWISS-PROT and TREMBEL 1. Introduction Protein sequence databases are biological databases that store information about amino acid sequences of proteins, along with their functional, structural, and biochemical characteristics. Since proteins are the functional molecules of the cell, protein databases are essential for understanding gene expression, metabolism, enzymatic activity, signaling pathways, and evolution. Protein sequence databases mainly contain data derived from translated nucleotide sequences and experimental protein studies. 2. Types of Protein Sequence Databases Protein sequence databases are broadly classified into: A. Primary Protein Databases Contain original protein sequence data Minimal or no manual annotation B. Secondary Protein Databases Derived from primary databases Provide curated functional and structural information C. Composite Protein Databases Combine protein data from multiple sources Reduce redundancy 3. Protein Informati...

Biological Databases – Types of Data and Databases Nucleotide Sequence Databases (EMBL, GenBank, DDBJ) 1. Introduction Biological databases are systematic, computerized collections of biological information that allow efficient storage, retrieval, updating, and analysis of large volumes of biological data. With the advent of genome sequencing, molecular biology, and bioinformatics, biological databases have become essential tools in biological research. These databases support studies in genomics, proteomics, evolutionary biology, taxonomy, medicine, agriculture, and biotechnology. 2. Types of Data Stored in Biological Databases Biological databases store diverse types of biological information, including: 1. Sequence Data DNA sequences RNA sequences Protein sequences 2. Structural Data Three-dimensional structures of proteins Nucleic acid structures 3. Functional Data Gene functions Enzyme activity Regulatory elements 4. Genomic Annotation Data Gene location Exons, introns Promoters a...

Reg. No.......  Name......... G-5263 Fourth Semester M.Sc. Degree Examination, September 2019 Botany Special Paper II - Elective BO 242 a: BIOTECHNOLOGY (2013 Admission onwards) Max. Marks: 75 1. Answer the following questions: 1. Humulin 2. YAC 3. Cybrids 4. Hybridomas 5. IPR 6. Gene therapy 7. C DNA library 8. AFLP 9. Hairy root culture 10. Somacional variation (10 x 1=10 Marks) II. Answer the following questions in not more than 50 words : 11. (a) What are immobilized enzymes? What is its advantage? OR (b) Write a short note on molecular farming. 12. (a) Give an account of bioprocess technology for the production of secondary metabolites. OR (b) What are bioreactors? How it operates? 13. (a) What are probiotics?. How do they work? OR (b) Discuss the methodology and application of western blotting. 14. (a) Briefly explain the application of protoplast culture OR (b) Write a short note on gene therapy 15. (a) What are reporter genes? Discuss its utility in transformation studies O...

Reg. No....... Name:........ G-5262 Fourth Semester M.Sc. Degree Examination, September 2019 Botany BO 241: BIOINFORMATICS (2013 Admission onwards) Time: 3 Hours I. Answer the following questions: 1. Contiguous sequences 2. Protein Motif 3. INDEL 4. DOTPLOT 5. J PRED 6. Phylogram 7. EST 8. Query sequence 9. TIGR 10. CLUSTAL (10 x 1 = 10 Marks) II. Answer the following questions in not more than 50 words: 11. (a) Describe protein atlas and its significance in the development of bioinformatics. OR (b) Contribution of Frederick Sanger in advancement of proteomics. 12. (a) Describe Entrez with its significance. OR (b) Describe the advantages of EST search in gene sequencing programme. 13. (a) What are the salient features of UniProt KB (SWISSPROT). OR (b) Describe the features GenBank. 14. (a) Describe the concept of evolutionary tree. OR (b) Describe RasMol. 15. (a) Significance of BioPerl software in Human Genome project OR (b) Describe boutique databases. (5 x 2 = 10 Marks) III. Answer ...

J-4882 Reg. No......  Name :......... Fourth Semester M.Sc. Degree Examination, May 2020 Botany BO 242 a - BIOTECHNOLOGY (2013 Admission Onwards) Max. Marks: 75 I. Answer the following questions 1. Define Palindromic sequences. 2. What is meant by Probiotics? 3. Explain the terms YAC and BAC. 4. Define Klenow fragment. 5. What is meant by Bio piracy? 6. Give the speciality of ddNTPs. 7. Briefly explain Somatostatin. 8. What are the advantages of Filter sterilization? 9. Give the significance of Star activity. 10. Give significance of Redifferentiation. (10 x 1 = 10 Marks) II. Answer the following questions in not more than 50 words 11. (a) Differentiate Taq DNA polymerase and DNA polymerase 1 used in thermal cycler. OR (b) Explain any one hybridization based molecular marker. 12. (a) Differentiate RFLP and RAPD. OR (b) Explain 2D-electrophoresis. 13. (a) Give a note on Somatic embryogenesis. OR (b) Explain the role of protoplast culture in cytoplasmic male sterility. 14. (a) What m...

Reg. No.: Name: J-5602 Fourth Semester M.Sc. Degree Examination, January 2021. Botany Special Paper II - Elective BO 242 a - BIOTECHNOLOGY (2013 Admission Onwards) (Special Examination) Time: 3 Hours 1. Answer all questions: 1. What are expression vectors? 2. Expand and explain EcoRI. 3. What is indirect regeneration in tissue culture? 4. Differentiate between dedifferentiation and redifferentiation. 5. What is meant by site directed mutagenesis? 6. What are the fundamental abilities of plants that determine the success of plant tissue culture? 7. What is bioremediation? 8. Define gametoclonal variation. 9. What are bioinsecticides? What are the advantages of it? 10. What is the difference between batch and continuous fermentation? (10 × 1 = 10 Marks) II. Answer the following questions in not more than 50 words. 11. (a) Explain the need for hardening the tissue culture regenerated plantlets. OR (b) Describe lipofection. 12. (a) Write a brief note on micropropagation. OR (b) Explain how...

Reg. No.: Name: J-5601 Fourth Semester M.Sc. Degree Examination, January 2021 Botany BO 241 BIOINFORMATICS (2013 Admission Onwards) (Special Examination) Time: 3 hours 1. Answer the following questions. 1. SCOP. 2. FASTA. 3. Gene finding. 4. GSDB. 5. TIGR. 6. BLOSUM. 7. DBMS. 8. Conserved sequences. 9. Modular proteins. 10. Autodock. (10x1 = 10 Marks) II. Answer the following questions in not more than 50 words. 11. (a) Briefly describe the salient features of genbank. OR (b) Describe DOTPLOT. 12. (a) Describe the application of Clustal software. OR (b) Differentiate between global alignment and local alignment. 13. (a) What is a specialized database? OR (b) What is meant by threading in proteomics? 14. (a) Describe the software used in constructing dendrograms. OR (b) Describe RASMOL with its advantage. 15. (a) Describe dynamic programming methods. OR (b) Describe two methods of tertiary structure prediction of proteins. III. Answer the following questions in not more than 150 words. ...