Table 2.
Questions asked at the level of | Analysis | Bioinformatics skills/tools | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
I3Ua | Focal taxa | Evolution | Behavior | Physiology | Morphology | Cell | Molecular | Biochemistry | Functional | Comparative | Metagenomic | Species-specific DNA database | Multi-species genome browser | Protein modeling | BLAST/alignment | Phylogenetics | Programming |
A | Brassica | √ | √ | √ | √ | ||||||||||||
B | Human | √ | √ | √ | |||||||||||||
C | Wood frog | √ | √ | √ | √ | ||||||||||||
D | Fish/vertebrates | √ | √ | √ | √ | √ | √ | ||||||||||
E | Fish/vertebrates | √ | √ | √ | √ | √ | √ | ||||||||||
F | Xenopus | √ | √ | √ | √ | √ | √ | ||||||||||
G | Pea/various | √ | √ | √ | √ | √ | |||||||||||
H | Eubacteria | √ | √ | √ | √ | √ | √ | ||||||||||
I | Mouse | √ | √ | √ | √ | √ | √ | √ | |||||||||
J | Worm | √ | √ | √ | √ | √ | |||||||||||
K | Dog | √ | √ | √ | √ | √ | √ | √ | |||||||||
L | Various | √ | √ | √ | √ | √ | √ | √ | |||||||||
M | Various | √ | √ | √ | √ | √ | √ | ||||||||||
N | N/A | √ | √ | √ | √ |
aLetters denote I3U units as follows: A: Reconstructing the Evolution of Cauliflower and Broccoli; B: Human Single Nucleotide Polymorphism Determination; C: Local Population Structure and Behavior of the Wood Frog Rana sylvatica; D: Comparison of Protein Sequences: BLAST Searching and Phylogenetic Tree Construction; E: Phylogenetic Analysis of Bony Fishes: Morphological and mtDNA Sequence Comparisons; F: Molecular Evolution of Gene Families; G: Exploring the Chamaecrista fasciculata Gene Space; H: Metagenomic Analysis of Winogradsky Columns; I: Behavior, Neuroanatomy, Genomics: What Can We Learn from Mouse Mutants?; J: Expression of Gerontogenes in Neurons: A Comparative Genomic Approach to Studying the Role of the Nervous System in Lifespan/Aging; K: Comparison of a Highly Polymorphic Olfactory Receptor Gene Subfamily in Genetically Diverse Dog Breeds; L: Integrative Activities to Study the Evolution of Nervous System Function; M: Modeling Molecular Evolution; N: Constructing and Using a PAM-Style Scoring Matrix.