Syllabus
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Course Code: OE Elective-II OE-CS-403 Course Name: Bioinformatics |
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| MODULE NO / UNIT | COURSE SYLLABUS CONTENTS OF MODULE | NOTES |
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| 1 | Databases Sequence Databases: introduction of Databases, primary and secondary databases, nucleotide and protein sequence databases: Genbank, EMBL, DDBJ, Swissprot, pfam, Block, PRI Structure Databases: Introduction to structures. PDB (Protein Data bank) Molecular Modeling database at NCBI. , visualizing structural information, database structure viewers. Sequence and Structure File Formats; The Entrez system: Integrated information axis, Information retrieval from biological database, sequence database beyond NCBI. Medical databases. |
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| 2 | Sequence Alignment AND Database Searches Introduction, the evolutionary basis of sequence alignment, Type of Aligmnents, Pair-wise Alignment, Multiple Alignment, The modular nature of proteins, Optimal alignment methods, substitution scores and gap penalties, statistical significance of alignment. FASTA, BLAST, low-complexity regions, repetitive elements, Tool of multiple sequence alignment: CLUSTAL W/X, progressive alignment method. Phylogenetic Analysis: Elements of phylogenetic models, phylogenetic data analysis: alignment, substitution model building, tree building and tree evaluation, building the data model (alignment), determining the substitution model, tree- building methods, searching for trees, rooting trees, evaluation trees and data, phylogenic software (PHYLIP). phylogenetics online tool. |
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| 3 | Sequence Analysis Using Software Resources : Introduction. The Wisconsin package, the Seq Lab environment, analyzing sequences with operations and Wisconsin package programmes, viewing output, monitoring programme progress and troubleshooting problems, annotating sequences and graphically displaying annotations in the Seqlab Editor, saving sequences in the Seq Lab Editor, Example of analysis that can be undertaken in Seqlab, extending Seqlab by including programmes that are not part of the Wiscosin package. |
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| 4 | Plasmid Mapping And Primer Design Restriction mapping, Mac Vector and OMIGA. Gene construction kit. Vector NTI, primer design for PCR Sequencing, primer design programs and software. |
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