RDWU Bioinformatics

Syllabus

UNIT- III

• Biological databases: nucleic acid & protein databases, primary, secondary, functional and composite databases,

• Data analysis: Data access, retrieval and submission, limitations of existing databases

• Global webservers for databases: NCBI, EMBL and DDBJ 

UNIT- IV

• Sequence alignment: Local alignment, Global alignment, tools for sequence alignment.

• Scoring matrices: PAM, BLOSUM, Gaps and penalties, Dot plots.

• Dynamic programming approach: Needleman and Wunsch Algorithm, Smith and Waterman Algorithm, Hidden Markov Model

UNIT- V

• Genome sequencing and Assembly: Sequencing and analysis of large genomes, gene prediction and functional annotation.

• Visualization tools:  genome comparison, Artemis, VISTA, visualization tools such as PyMol and VMD.

• Molecular modelling: different types of protein chain modelling: ab initio, homology, hybrid, loop; Modelling parameters and considerations, Model analysis and validation