Download DNA barcodes

Introduction to Bioinformatics
Resources for DNA Barcoding
DNA Barcoding
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DNA barcoding is a tool for rapid
species identification based on DNA
sequences
DNA barcodes consist of a
standardized short sequence of DNA
(400–800 bp) that in principle should
be easily generated and characterized
for all species on the planet.
DNA barcoding aims to use the
information of one or a few gene
regions to identify all species of life,
General Steps:
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DNA amplification of DNA fragment
DNA sequencing and assembly
species identification
molecular phylogenetic analysis
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Bioinformatics
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Bioinformatics is defined as an interdisciplinary research area that
applies computer and information science to solve biological
problems.
DNA Sequencing
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DNA Sequence Trace
• Four color chromatogram
showing the results of a
sequencing run.
• The characters below
each peak represents the
softwares attempt at
identifying the correct
nucleotide.
• Errors commonly occur
near the beginning and
the end of any read.
Read Assembly
• CAP3 – an accessory application of BioEdit and assembles DNA or RNA
sequences by identifying overlapping regions between multiple DNA or RNA
sequences and merges (assembles) them.
• Assembled reads are referred to as contigs, short for contiguous sequence.
Basic Local Alignment Search Tool
(BLAST)
• Compares a query sequence to a database collection of
sequences.
• Retrieves significantly similar sequences
• Blast tools: blastn, blastp, blastx, tblastn, tblastx
Multiple Sequence Alignments
• An alignment between 3 or more sequences
• The algorithm identifies a series of characters that are in the same
order in both sequences.
• The assumption is that all sequences in a multiple sequence
alignment are evolutionarily related.
• Highlights insertion/deletion and amino acid substitution events
Molecular Phylogenetics
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Molecular Phylogenetics: the study of the evolutionary relationships of genes and other
biological macromolecules by analyzing mutations at various positions in their sequences and
developing hypotheses about the evolutionary relatedness of the biological molecules.
Gene phylogeny: tree branching pattern representing the evolution of a group of related genes
Species phylogeny: tree branching pattern representing the evolution of a group of related
species
Steps:
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(1) Create a multiple sequence alignment of DNA or protein sequences
(2) Analyze multiple sequence alignment using 1 of 5 different analyses methods.
Molecular Phylogenetics: MSA analysis
• Five common molecular phylogenetic methods: UPGMA,
Neighbor Joining, Maximum Parsimony, Maximum Likelihood
• The most accurate method is Maximum Likelihood, but is
also the slowest.
• The most commonly used is Neighbor Joining, which is faster,
but not as accurate as Maximum Likelihood
Molecular Phylogenetics: MSA analysis
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Tree topology: branching pattern in the tree
Taxa – the end point of a branch representing the sequences used in the analysis.
Branch – horizontal lines conneting two nodes, or nodes and taxa
– Cladogram – branch lengths represent evolutionary change
– Phylogram – branch lengths are meaningless
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Node – bifurcating (or multifurcating) points in the tree
Scale Bar – indicates degree of divergence represented by a given branch length.
Maximum Likelihood measures average number of substitutions per site.
Molecular Phylogenetics: MSA analysis
• Bootstrapping: statistical technique that tests the sampling errors of a
phylogenetic tree.
• Bootstrap values are measures of confidence of the tree topology. The
higher the value the more the relationship can be trusted.
The End
• Lets do a little bioinformatics