Question

1. Briefly describe how you would generate a “neighbor join” phylogenetic tree.

2. Briefly describe the classification for different types of Biological Sequence Databases.

3. Describe the computational methods commonly used to detect genes that have been acquired via Horizontal Gene Transfer (HGT).

Please andwer these 3 questions :)

thank you

Answer 1

1. Neighbor joining is an bottom up clustering method which requires knowledge of distance between each pair of taxa to create phylogenetic tree based on DNA or protein sequence data. Neighbor joining keeps the track of nodes on a tree rather than taxa or cluster of taxas. The initial tree is star tree which is unresolved with raw data provided in the form of distance matrix i. e the distance between each pair of taxa. During this the separation between each pair of node is adjusted based on the average divergence from all other nodes. The tree is constructed by linking least distant pair of nodes in the matrix. When the two nodes are linked their common ancestral node is added to the tree. The terminal nodes with their respective branches are removed from the tree. This purning process reduces the tree size and the newly added common ancestral node is converted into terminal node. At each stage in the process two terminal nodes are removed and a new node is added. This procedure is repeated till only two node remain separated by a single branch.

2. The answer for classification for different types of biological sequence databases is uploaded in the form of figure.

3. Horizontal gene transfer is a fundamental mechanism in which one organism is able to directly transfer genetic material between distant species. Identification of HGT through computational methods rely on investigating sequence composition (parametric method) or evolutionary history of genes (phylogenetic method). In sequence composition based method average deviation in genome is identified such as GC content or codon usage; whereas in evolutionary history based method genes whose evolutionary history is different from that of host species is identified. Parametric method rely on the genome under study where HGT might have occured in its lineage. If a fragment of genome is deviating from the genomic signature, this is a sign of potential horizontal transfer. Commonly used genomic signature are nucleotide composition, oligonucleotide frequencies or structural features of the genome. Phylogenetic methods integrate information from multiple genomes using model of evolution. It can be done explicitly by constructing the gene tree and comparing it with the reference tree or implicitly by examining different aspects correlating with the evolutionary history of that gene.