1. Bioinformatics and Phylogenetic Analysis
Edgar Scott
Multicampus Bioinformatics Education Specialist

2. What is Bioinformatics
Interdisciplinary field that combines principles and techniques from computer science, probability and statistics, and linguistics to the study of genomic and proteomic sequences.
Biological database for storing and organizng DNA and protein sequences
Computational tools for analyzing sequences

3. Phylogenetic Analysis and Bioinformatics
Phylogenetics – study of evolutionary relationships
Phylogenetic trees used to represent evolutionary relationships
Use of protein or DNA sequences to detect relationships versus morphological characters
Bioinformatics provides both sequence repositories and sequence analysis software.

4. Overview Acquiring Data Set Analyzing Data Set
Text searching at the National Center for Biotechnology Information (NCBI)
Sequence similarity and homology
Sequence similarity searching with Basic Local Alignment Search Tool (BLAST)
Analyzing Data Set
Phylogenetic Analysis with Molecular Evolutionary Genetics Analysis (MEGA) 3.1 software
Build multiple sequence alignments of sequences using ClustalW
Build phylogenetic trees

5. Text Searching at NCBI
NCBI maintains provides molecular information and bioinformatic tools to the scientific community
GenBank – an archival DNA and protein sequence database
RefSeq – a curated DNA and protein sequence database
Entrez Gene – a gene centered database

6. Sequence Similarity and Homology
Homology – sequence that share a common ancestral sequence
Paralogs – arise via gene duplication
Orthologs – arise via speciation event
Xenologs – arise via gene transfer
Evolutionarily related sequences have similar sequences.
Sequence differences correspond to amount of change that has occurred since they last shared a common ancestral sequence.

7. Sequence Alignments
Sequence Alignment – a process that identifies a series of characters or character patterns that are in the same order in both sequences.
Pairwise Global alignment
Pairwise Local alignment
Optimal alignment – an alignment between sequences in which the number of matching characters are maximized and the mismatching characters are minimized.
Quantifying alignments
Alignment score of the optimal alignment
Percent identity scores
Percent similarity scores

8. Sequence Similarity Searching
Basic Local Alignment Search Tool (BLAST)
Blastp, Blastn, Blastx, Tblastn, & TblastX
Local alignments are reported
Expectation Value – the number of times an investigator can expect to find an alignment that has an alignment score as good or better than the alignment score under consideration.

9. Steps to Build a Tree Build a multiple sequence alignment of data set.
Analyze multiple sequence alignment using either distance based methods or character based methods.

10. Molecular Evolutionary Genetics Analysis (MEGA) 3.1
Phylogenetic Analysis program
Constructs multiple sequence alignment using ClustalW
Provides tree building methods
Distance based Methods
UPGMA
Neighbor-joining method
Minimum Evolution
Character based Method
Maximum Parsimony
Provides a great help document!

11. Multiple Sequence Alignment
Multiple Sequence Alignment – an alignment between three or more sequences.
Computationally classified as NP-hard
Programs
ClustalW – fast, applies a progressive method
T-Coffee – slower, applies an advanced progressive method
Dialign – slow, applies an iterative method
Combine – combines multiple sequence alignments

12. Tree Building methods UPGMA, Neighbor-Joining, Minimum Evolution
Distance based methods
Analyze the multiple sequence alignment to calculate a distance matrix.
Clustering algorithm analyzes the distance matrix to determine which sequences should be clustered.
Maximum parsimony
Character based method
Analyze the multiple sequence alignment to create a tree whose tree length has been minimized.

13. Tree Reliability
Bootstrapping – method for assessing the reliability of trees.
Steps
The original data set is resampled several times (e.g. 1000).
For each resampling, a tree is built
The trees created from the resampling iterations are compared to the original tree.

14. Review Acquiring Data Set Analyzing Data Set
Text searching at the National Center for Biotechnology Information (NCBI)
Sequence similarity and homology
Sequence similarity searching with Basic Local Alignment Search Tool (BLAST)
Analyzing Data Set
Phylogenetic Analysis with Molecular Evolutionary Genetics Analysis (MEGA) 3.1 software
Build multiple sequence alignments of sequences using ClustalW
Build phylogenetic trees