Analysis of data from an automated DNA
sequencer
Data
Extraction & Analysis
cf. Investigation #3 in Bio2250
w/ CHROMAS©
Sequencher © from GeneCodes (for Mac & PC platforms)
Multiple, simultaneous Chromatogram editing
Automated alignment to reference sequence
e.g., CLUSTAL
Contig
Assembly
generation of
continuous sequence from overlapping, contiguous fragments
Export of "finished" sequences to
NEXUS format for PAUP© (for Mac platform): D. Swofford et al.
& MEGA© (for PC): M. Nei et al.
Data
Interpretation
GenBank BLAST
search: to identify an unknown
sequence [e.g., cDNA inserts]
Interpreting BLAST
output
e-values
comment on "complexity"
Phylogenetic Analysis
Inter-specific comparisons wrt evolution = phylogenetics
Intra-specific comparisons wrt geography &
ecology = phylogeography
Phenetic & cladistic
approaches
Parsimony
methods [e.g., maximum
parsimony]
Distance
methods [e.g., UPGMA]
Likelihood methods
[Bayesian
methods]
Sequencher
project
in
2010
Given: unedited caribou DNA sequence data from
mtDNA Cytb & CR loci
MHC DRB locus
Required:
Assemble contigs against corresponding
reference sequences
Edit contigs, identify SNPs
Export consensus sequence for each individual
[Compare with other
homologous sequences in MEGA]
Compare
Newfoundlan
caribou vs
European reindeer
Evaluate hypotheses:
Caribou &
Reindeer differ genetically at mtDNA and nucDNA loci
Text
material
©
2010 by Steven M. Carr