Glossary

A list of terms used in various pages in this wiki that may need clarification.

Genomic Evolution Terminology

• Biased fractionation
• Chromosome Rearrangement
• Conserved Non-Coding Sequence (CNS)
• Contig
• Deletion
• Diploidization
• DNA alignment
• Dotplot
• Fractionation
• Genespace
• Genomic Feature
• High-scoring segment pair (HSP)
• Homolog
• Homeolog
• Insertion
• In-Paralog
• Inversion
• Local Gene Duplication
• Neofunctionalization
• Ortholog
• Out-Paralog
• Paleopolyploid
• Paralog
• Perfect Ortholog
• Plant paleopolyploidy
• Polyploid
• Protein alignment
• Repeat sequence
• Segmental Duplication
• Speciation
• Subfunctionalization
• Synonymous/Nonsynonymous Mutations (Ks/Ka)
• Syntelog
• Synteny
• Tandem Gene Duplication
• Translocation
• Transposition
• Whole Genome Duplication

Methodology

• Collinear Gene Order for detecting syntenic regions
• Flanking Gene Method for detecting gene loss and transposition events
• Useful divergence for comparing genomic regions
• Data visualization: data abstraction for human perception

Algorithm Terms

• E-value
• Global alignment
• Local alignment
• Score
• Scoring Matrix
• Word size

Application Programming Interface (API) Terms

• Chromosome
• Dataset
• Dataset group
• Genomic feature
• Organism description

CoGe Tools

• CoGe NCBI Loader