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Basic Applied Bioinformatics
Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal
- English
- ePUB (mobile friendly)
- Available on iOS & Android
Basic Applied Bioinformatics
Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal
About This Book
An accessible guide that introduces students in all areas of life sciences to bioinformatics
Basic Applied Bioinformatics provides a practical guidance in bioinformatics and helps students to optimize parameters for data analysis and then to draw accurate conclusions from the results. In addition to parameter optimization, the text will also familiarize students with relevant terminology. Basic Applied Bioinformatics is written as an accessible guide for graduate students studying bioinformatics, biotechnology, and other related sub-disciplines of the life sciences. This accessible text outlines the basics of bioinformatics, including pertinent information such as downloading molecular sequences (nucleotide and protein) from databases; BLAST analyses; primer designing and its quality checking, multiple sequence alignment (global and local using freely available software); phylogenetic tree construction (using UPGMA, NJ, MP, ME, FM algorithm and MEGA7 suite), prediction of protein structures and genome annotation, RNASeq data analyses and identification of differentially expressed genes and similar advanced bioinformatics analyses. The authors Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, and Mir Asif Iquebal are noted experts in the field and have come together to provide an updated information on bioinformatics.
Salient features of this book includes:
- Accessible and updated information on bioinformatics tools
- A practical step-by-step approach to molecular-data analyses
- Information pertinent to study a variety of disciplines including biotechnology, zoology, bioinformatics and other related fields
- Worked examples, glossary terms, problems and solutions
Basic Applied Bioinformatics gives students studying bioinformatics, agricultural biotechnology, animal biotechnology, medical biotechnology, microbial biotechnology, and zoology an updated introduction to the growing field of bioinformatics.
Frequently asked questions
Information
SECTION V
Molecular Phylogenetics
CHAPTER 21
Construction of Phylogenetic Tree: UnweightedâPair Group Method with Arithmetic Mean (UPGMA)
21.1 INTRODUCTION
- Unweighted: It indicates equal contribution of all the pairâwise distances. There is no weighting of any specific taxaâpairs to indicate a different evolutionary rate compared with another pair(s). This is the opposite of the WeightedâPair Group Method with Arithmetic mean (WPGMA).
- Pairâgroups: Any two taxa or any two clusters (clade) or one taxon and a cluster are always combined in pairs (that is, interpreted as dichotomies).
- Arithmetic mean: Pairâwise distance of each group is the mean distance to all members of that group.
21.2 ASSUMPTIONS
- Constant rate of evolution (i.e., mutationârate) amongst all the sequences.
- Distance data are ultrametric: This enables clustering by satisfying the âthree point conditionâ to generate the tree.
TERMINOLOGIES AND POINTS
- Neighbors: the external nodes with the smallest number of mismatches.
- Ultrametric: in distance methods, an ultrametric tree is characterized by a âThree point conditionâ, where three points (a, b, c) satisfy the condition for the distance...