Bioinformatics Virtual Lab II : Biotechnology and Biomedical Engineering : Amrita Vishwa Vidyapeetham Virtual Lab

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Bioinformatics Virtual Lab II

This virtual laboratory is for undergraduate and postgraduate students to get a deeper understanding on the analysis of sequence data, its alignment and the evolutionary relationship. The exercises mainly deal with the different algorithms in sequence alignment and provides a computational exploration to the use of various tools used for sequence alignment.

	Global alignment of two sequences - Needleman-Wunsch Algorithm A commonly used algorithm to perform global alignment among the two sequences
	Smith-Waterman Algorithm - Local Alignment of Sequences A popular algorithmic approach to perform local alignment among the two sequences.
	Pairwise Sequence Alignment using BLAST To find out the sequences which are similar to the query sequences.
	Pairwise sequence alignment using FASTA To find the sequences which are similar to the given query sequences using FASTA.
	Aligning Multiple Sequences with CLUSTAL W The best alignment tool for a group of sequences to align globally and finds the evolutionary relationship between the sequences.
	Construction of Cladogram Constructing a cladogram using PHYLIP to represent the relation between the organisms.
	Phylogenetic Analysis using PHYLIP - Rooted trees Constructing a rooted phylogenetic trees using PHYLIP
	Phylogenetic Analysis using PHYLIP - Unrooted trees Constructing an unrooted phylogenetic trees using PHYLIP
	Genome Annotation and Multiple Sequence Allignment. Genome annotation helps in the identification of the non coding(which do not code for protein) and coding(gene) and that genome alignment can can help us understand the evolutionary history.