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.

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