Abstract
There are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non-coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text.
Original language | English (US) |
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Pages (from-to) | 661-673 |
Number of pages | 13 |
Journal | Plant Journal |
Volume | 53 |
Issue number | 4 |
DOIs | |
State | Published - Feb 2008 |
Externally published | Yes |
Keywords
- CNS
- Fractionation
- Plant comparative genomics
- Synteny
ASJC Scopus subject areas
- Genetics
- Plant Science
- Cell Biology