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Indian Institute of Science Education and Research Berhampur
BIO 402: Bioinformatics (4)
Introduction to bioinformatics, overview, concepts, utility, scope, applications, skills needed, sequences, biological data; Databases, web resources: NCBI- Entrez, PubMed, GenBank, data organization and retrieval using FTP from NCBI, DDBJ, UCSC, PDB, SwissProt, KEGG, and web resources; Sequence formats: FASTA, GenBank, EMBL, PDB, XML, Medline, GCG, etc. Conversion from one format to another, tools available for format interconversion; Sequence alignment algorithm and tools: Introduction to sequence alignment, homology, similarity, identity. Local and global alignments, multiple sequence alignments, insertions, deletions, gaps, Needleman-Wunsch algorithm, Dot matrix method, dynamic programming algorithm, scoring matrices- PAM and BLOSUM, Blast, Blat, Clustalw, MAFFT, BLOCKS, etc.; Prediction of genes and annotation methods: Concept of genes, challenges in gene prediction, ORFs, reading frames, codons and codon bias, genetic code, commonly used gene prediction methods- ORF finder, Glimmer, GeneMark, Metagene, etc. Annotation using homology-based alignment using Blast or Blat, COGs and Gene ontology based functional annotation; Phylogenetic analysis: concepts and terminologies, commonly used phylogenetic methods such as PHYLIP, MEGA. Introduction to rRNA, taxonomy and taxonomic classification. Maximum parsimony method, Distance methods, Neighbor-joining methods; Protein classification and structure prediction: Introduction to domains, motifs, fold, family, Helices, beta-sheets, loops, coils. Primary, secondary and tertiary structure. Structure visualization tools such as RasMol; Genome analysis: Introduction to genomes and packages for genomic analysis such as EMBOSS; Introduction to Linux and Perl.
Suggested Books:
- Bioinformatics- Sequence and Genome Analysis by David W. Mount; Cold Spring Harbor Laboratory Press,U.S.; 2nd Revised edition edition; 2004.
- Introduction to Computational Genomics by Nello Cristianini and Matthew W. Hahn; Cambridge University Press; 2007.
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