RDWU Bioinformatics
Slides/Resources
Unit - III
Unit - IV
Pairwise Alignment: Gaps & Substitution Matrixes📗
Global & Local Alignment📗
Basic Local Alignment Search Tool📗 BLAST Exercise📜
Unit V
Sequence & Structure Motifs📗
Structure Classification📗
Protein Structure Prediction📗
Comparative (Homology) Modelling📗
Adv. Protein Structure Prediction📗
Secondary Structure Prediction📗
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