DNA Data Extraction, Analysis, & Interpretation

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