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Secondary Databases (PROSITE, PRINTS, BLOCKS)

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 ...
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••CLASSIFICATION OF ALGAE - FRITSCH

      MODULE -1       PHYCOLOGY  CLASSIFICATION OF ALGAE - FRITSCH  ❖F.E. Fritsch (1935, 1945) in his book“The Structure and  Reproduction of the Algae”proposed a system of classification of  algae. He treated algae giving rank of division and divided it into 11  classes. His classification of algae is mainly based upon characters of  pigments, flagella and reserve food material.     Classification of Fritsch was based on the following criteria o Pigmentation. o Types of flagella  o Assimilatory products  o Thallus structure  o Method of reproduction          Fritsch divided algae into the following 11 classes  1. Chlorophyceae  2. Xanthophyceae  3. Chrysophyceae  4. Bacillariophyceae  5. Cryptophyceae  6. Dinophyceae  7. Chloromonadineae  8. Euglenineae    9. Phaeophyceae  10. Rhodophyceae  11. Myxophyce...
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❥ Southern Blotting Notes

Southern Blotting  ❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥  Introduction Southern blotting is a molecular biology technique used for the detection of specific DNA sequences in a complex mixture of DNA. It was developed by Edwin M. Southern in 1975. The method involves restriction digestion of DNA, separation by gel electrophoresis, transfer (blotting) onto a membrane, and hybridization with a labeled DNA probe. Principle of Southern Blotting The technique is based on the principle of complementary base pairing. A single-stranded labeled DNA probe hybridizes specifically with its complementary DNA sequence immobilized on a membrane. Detection of the label confirms the presence and size of the target DNA fragment. Steps Involved in Southern Blotting. 1. Isolation of DNA Genomic DNA is extracted from cells or tissues. DNA must be pure and intact to ensure accurate results. 2. Restriction Enzyme  Digestion DNA is digested using specific restriction endonucleases. Produces DNA f...
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❃LC-MS (LIQUID CHROMATOGRAPHY – MASS SPECTROMETRY)

LC-MS (LIQUID CHROMATOGRAPHY – MASS SPECTROMETRY)  ┏━━━━━ •❃°•°❀°•°❃•━━━━•━━━┓ 1. INTRODUCTION LC-MS is a hyphenated analytical technique combining Liquid Chromatography (LC) and Mass Spectrometry (MS). It is used for separation, identification, and quantification of compounds in complex mixtures. LC separates analytes based on polarity, size, or charge, while MS detects molecules based on mass-to-charge ratio (m/z). Developed in the 1970s–1980s, LC-MS is now widely used in pharmaceutical, clinical, environmental, and food analysis. Importance : Detects trace levels of compounds (ng–pg range) Analyzes non-volatile, thermally labile compounds that cannot be analyzed by GC-MS Provides structural information through mass fragmentation Example: Detection of drugs in plasma, protein identification in proteomics, pesticide residue analysis in food. 2. COMPONENTS OF LC-MS The LC-MS system has three main parts: A. Liquid Chromatograph (LC) Function: Separates components of a mixture befor...
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Fourth Semester M.Sc. Degree Examination, June 2022BotanySpecial Paper II - ElectiveBO 242 a: BIOTECHNOLOGY

Reg. No.: Name: N-6273 Fourth Semester M.Sc. Degree Examination, June 2022 Botany Special Paper II - Elective BO 242 a: BIOTECHNOLOGY Time: 3 Hours (2019 Admission Onwards) Max. Marks: 75 1. Instruction: Draw diagrams and illustrate with examples wherever necessary. Answer the following questions. 1. What are the desirable features of a cloning vehicle? 2. What is a palindrome? 3. What is the significance of Ori C site? 4. What is the actual function of restriction enzymes in a bacterial system?  5.Name any two bacteria and fungi used for alcohol fermentation. 6. What is a starter culture? 7. What are adapters? 8. What are probes? 9. What is biopiracy? 10. Define cybrids. (10 x 1 = 10 Marks) II. Answer the following questions in not more than 50 words .  11. (a) Why is callus culture a prerequisite for somaclonal variations? OR (b) How is virus elimination done via plant tissue culture? 12. (a) How is aeration maintained in a bioreactor? OR (b) What are the methods available f...
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Intellectual Property Rights (IPR) – Detailed Notes

Intellectual Property Rights (IPR) – Detailed Notes 1. Introduction Intellectual Property Rights (IPR) are legal rights granted to creators and inventors over their creations or inventions. They protect innovation and creativity, providing the owner exclusive rights to use, sell, or license their creation. IPR encourages research, development, and economic growth by rewarding creativity. 2. Importance of IPR Protects inventions, designs, and creative work. Prevents unauthorized use, copying, or commercialization. Encourages innovation and research. Provides financial benefits to inventors through licensing or royalties. Supports economic growth and competitiveness. Safeguards traditional knowledge and biodiversity. 3. Types of Intellectual Property Rights A. Patents Definition: Exclusive right granted to an inventor for a new invention for a limited period (usually 20 years). Requirements: Novelty – must be new and not published. Inventive step – non-obvious to someone skilled in the f...
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Fourth Semester M.Sc. Degree Examination, March 2021Time: 3 HoursBotanyBO 241: BIOINFORMATICS AND BIOPHYSICS(2019 Admission)

Fourth Semester M.Sc. Degree Examination, March 2021 Time: 3 Hours Botany BO 241: BIOINFORMATICS AND BIOPHYSICS (2019 Admission) 1. Answer the following questions. 1. Expand EMBL and DDBJ. 2. What do bootstrap values indicate? 3. What is multiple sequence alignment? 4. What is SNP? 5. Define transcriptome. 6. What is Smith Waterman algorithm? 7. Comment on Phylip. 8. What are the factors that determine the electrophoretic mobility of a particle? 9. Differentiate between resolution and resolving power of the microscope. 10. Which are the factors that determine the sedimentation of a component during centrifugation? (10 x 1= 10 Marks) II. Answer the following questions in not more than 50 words. 11. (a) What is the difference between rooted and unrooted phylogenetic tree? OR (b) What is ORF? What is its significance in functional genomics? 12. (a) Explain the use of GENSCAN. OR (b) Explain the assumptions in molecular clock hypothesis. 13. (a) Write a brief explanation on KEGG. OR (b) Co...
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Gene Transfer Technologies – Detailed Notes

Gene Transfer Technologies – Detailed Notes 1. Definition Gene transfer is the process of introducing foreign DNA or genes into the genome of a target organism or cell. It allows the expression of new traits, study of gene function, and production of therapeutic proteins. Also known as gene delivery or genetic transformation. 2. Principles of Gene Transfer Involves delivery of DNA or RNA into cells or organisms. DNA can be integrated into the host genome or remain episomal (non-integrated). The goal is stable or transient expression of the transferred gene. Key considerations: Vector – vehicle for carrying the gene Target cell – plant, animal, microbial, or human cells Delivery method – physical, chemical, or biological 3. Types of Gene Transfer Gene transfer can be broadly classified into: A. Natural Gene Transfer Occurs in nature between organisms: Transformation: Uptake of naked DNA by bacteria. Transduction: DNA transfer via viruses (bacteriophages). Conjugation: Transfer of plasmi...
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Fourth Semester M.Sc. Degree Examination, May 2020BotanyBO 241 BIOINFORMATICS(2013 Admission Onwards)

Reg. No.:....... Name:......... J-4881 Fourth Semester M.Sc. Degree Examination, May 2020 Botany BO 241 BIOINFORMATICS (2013 Admission Onwards) Max. Marks: 75 I. Answer the following questions. 1. What are Secondary biological databases? 2. What is a Locus? 3. State the importance of E-value in sequence alignment? 4. Write the expansion of PHYLIP. 5. Distinguish proteome and proteomics. 6. Describe optimal alignment. 7. Define clade in a phylogenetic tree. 8. What is PIR? 9. List out any two tool used for molecular docking. 10. Write the name of submission tool for NCBI. (10 x 1=10 Marks) II. Answer the following questions in not more than 50 words. 11. (a) Give a short note on GenBank format. OR (b) Write the difference between scaled and unscaled phylogenetic trees. 12. (a) What are the two classes of data of UniProt? OR (b) State the difference between Orthologous and Xenologous sequences 13. (a) Write a brief note on character based phylogenetic analysis. OR (b) What is the role of...
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Third Semester M.Sc. Degree Examination, January 2023 Botany BO 231 PLANT BREEDING, HORTICULTURE AND BIOSTATISTICS

Third Semester M.Sc. Degree Examination, January 2023 Botany BO 231 PLANT BREEDING, HORTICULTURE AND BIOSTATISTICS Time: Three Hours (2019 Admission Onwards) I. Answer the following questions. 1.What is green super rice? 2.What are the functions of ICAR-NBPGR? 3.Give the importance of floral biology in plant breeding. 4.How do you develop a synthetic variety? 5.Where can you find gene-for-gene relationships? 6.Describe the significance of biodiversity policy. 7.What is Olericulture? 8.Describe the advantages of in door garden. 9.What is Students's t-test? 10. Explain Ogive graph. (10 × 1 = 10 Marks) 11.Answer the following questions in not more than 50 words . 11. (a) Explain hybridization and mention it's procedure. OR (b) Write short notes on the concept of centers of origin proposed by Vavilov. 12. (a) Describe cytoplasmic male sterility and its uses. OR (b) Explain the role of interspecific and intergeneric hybridization. 13. (a) What is seed certification? How is it done? ...
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