How to usefully compare homologous plant genes and chromosomes as DNA sequences

Eric H Lyons, Michael Freeling

Research output: Contribution to journalArticle

232 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)661-673
Number of pages13
JournalPlant Journal
Volume53
Issue number4
DOIs
StatePublished - Feb 2008
Externally publishedYes

Fingerprint

Plant Chromosomes
Plant Genome
Plant Genes
Sequence Alignment
chromosomes
nucleotide sequences
genome
sequence alignment
Synteny
genes
Sequence Homology
Noise
sequence homology
Genome
genomics
Research

Keywords

  • CNS
  • Fractionation
  • Plant comparative genomics
  • Synteny

ASJC Scopus subject areas

  • Plant Science

Cite this

How to usefully compare homologous plant genes and chromosomes as DNA sequences. / Lyons, Eric H; Freeling, Michael.

In: Plant Journal, Vol. 53, No. 4, 02.2008, p. 661-673.

Research output: Contribution to journalArticle

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