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Course Contents

Introduction to bioinformatics; biological databases: design and structure - types and retrieval of nucleic acid (or genomic) or protein sequence information; BLAST, FASTA, local and global sequence alignment - pairwise, multiple; retrieval of protein parameters, secondary and tertiary structure. Computation of protein parameters; Identification of protein families and domains. Phylogenetic analysis; Gene primer designing, retrieval of gene SNPs; Prediction and retrieval of Proteins posttranslational modification; Overview of protein structure (RCSB PDB, PDBe, PDBj, BMRB) and models (All-atom models, Residue-based models, Simplified residue alphabets, Lattice models); Proteins structure analysis, docking of proteins with ligands analysis; Ramachandran; homology modeling. PRACTICALS: Practice of various softwares and databases including NCBI, PDB, EcoCyc, DDBJ, SWISS-PROT, TIGR, KEGG etc. Bioedit, Repeatmasker, PHRED, PHRAP, BLAST, Prosite/BLOCKS/PFAM, CLUSTALW, Emotif, RasMol, Oligo, Primer3, Molscript, Treeview, Alscript, Genetic Analysis Software, MEGA4.0 etc. RECOMMENDED BOOKS Punam K. Saha, Ujjwal Maulik. Advanced Computational Approaches to Biomedical Engineering. (Springer, 2014) Yin Yao Shugart. Applied Computational Genomics. (Springer, 2012) Arthur M. Lesk. Introduction to Bioinformatics. 4th edition. (Oxford university press, 2014) Jenny Gu, Philip Bourne (Eds). Structural Bioinformatics (Wiley-Liss, 2009) Marketa Zvelebil and Jeremy O. Baum. Understanding bioinformatics (Garland Science, Taylor and Francis Group, LLC, 2008)

Course Synopsis

To familiarize students with biological data mining from online databases and the use of various bioinformatics tools for extracting and processing biological data.

Course Learning Outcomes

To learn basic bioinformatic tools and how to utilize these in basic and applied research

Introduction to bioinformatics (video no. 1-10 and 17-20)

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BLAST, FASTA, local and global sequence alignment (Video no. 20-30+55-69)

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Phylogenetic analysis

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Primer designing

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Protein structure (Video no. 150-227)

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Protein family

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Posttranslational modifications

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Book Title : Essential Bioinformatics
Author : Jin Xiong
Edition : 1st printed version (2006)
Publisher : Cambridge
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Book Title : Basics of Bioinformatics
Author : Jiang et al.
Edition : 2013
Publisher : Springer
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Title : SNP (Notes)
Type : Other

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Title : Phylogenetics Notes
Type : Other

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Title : Expasy Tools Notes
Type : Other

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Title : Primer Design
Type : Other

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