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Introduction to Bioinformatics; History; Contentions and applications; Scope of bioinformatics;
Basic introduction to Computers, Programming languages, fundamentals of the UNIX/Linux
operating system-various open resources essential for bioinformatics; HPC & HTC; Role of
internet and WWW in Bioinformatics; Neural networks and artificial intelligence. Basic
biomolecular concepts: central dogma; Protein and amino acid, DNA & RNA Sequence, structure
and function; Biological Data generation methods and problem posed by it - mass spectrometry
and Edman degradation, Sanger‘s sequencing and Maxam–Gilbert sequencing; Introduction to
NGS platforms.

UNIT – II: (10 Hours)
Concepts of database; Database management systems (DBMS); Introduction to query language;
Index; Forms and Reports. Introduction to Bioinformatics data and databases:- Types of
Biological data: Genomic DNA, Complementary DNA (cDNA), Recombinant DNA (rDNA),
Expressed sequence tags (ESTs), Genomic survey sequences (GSSs), SNPs. Primary Databases:-
GenBank, EMBL, DDBJ, Composite Databases:-NRDB, UniProt, Literature Databases:- Open
access and open sources, PubMed, PLoS, Biomed CentralCentral. Sequence Databases :-
Nucleotide sequence Databases (GenBank, EMBL, DDBJ); Protein sequences Databases (Swiss-
ProtProt, TrEMBL, UniProt, UniProt Knowledgebase – UniProtKB, UniProt Archive –UniParc,
UniProt Reference Clusters –UniRef, UniProt Metagenomic and Environmental Sequences –
UniMES); Sequence motifs Databases:-Prosite, ProDom, Pfam, InterPro. Sequence file formats:-
fasta, fastq, sam/bam, vcf, gff; GenBank, PIR, aln/ClustalW2, GCG/MSF. Structure and derived
databases:- The primary structure databases (Protein Data Bank –PDB, Cambridge Structural
Database –CSD, Molecular Modeling Database -MMDB).
UNIT – III: (10 Hours)

The secondary structure databases (Structural Classification of Proteins –SCOP, Class
Architecture Topology Homology –CATH, Families of Structurally Similar Proteins –FSSP,
Catalytic Site Atlas –CSA. Molecular functions/Enzymatic catalysis databases (KEGG ENZYME
database, BRENDA).
Genome Databases:- Viral genome database (ICTVdb, VirGen), Bacterial Genomes database
(Genomes OnLine Database –GOLD, Microbial Genome Database-MBGD), Organism specific
Genome database (OMIM / OMIA, SGD, WormBase, PlasmoDB, FlyBase, TAIR), and Genome
Browsers (Ensembl, VEGA genome browser, NCBI-NCBI map viewer, KEGG, MIPS, UCSC
Genome Browser)Bioinformatics Database search engines:-Text-based search engines (Entrez,
SRS, DBGET /LinkDB). Sequence similarity based search engines (BLAST and FASTA). Motif-
based search engines (ScanProsite and eMOTIF). Structure similarity based search engines
(VAST and DALI). Proteomics tools at the ExPASy server; Data Submission.

PRACTICAL (30 Hours)

1. Understanding and use of web resources: NCBI
2. Retrieval of information from nucleotide and protein databases.
3. Basic commands of Windows, Unix and Linux operating systems
4. Similarity searches using tools like BLAST and interpretation of results
5. Use of different protein structure prediction tools
6. Sequence alignment