Genomics Inform.  2012 Mar;10(1):58-64. 10.5808/GI.2012.10.1.58.

Comparative Evaluation of Intron Prediction Methods and Detection of Plant Genome Annotation Using Intron Length Distributions

• Yang L
• Cho HG

• KMID: 2053286
• DOI: http://doi.org/10.5808/GI.2012.10.1.58

Abstract

Intron prediction is an important problem of the constantly updated genome annotation. Using two model plant (rice and Arabidopsis) genomes, we compared two well-known intron prediction tools: the Blast-Like Alignment Tool (BLAT) and Sim4cc. The results showed that each of the tools had its own advantages and disadvantages. BLAT predicted more than 99% introns of whole genomic introns with a small number of false-positive introns. Sim4cc was successful at finding the correct introns with a false-negative rate of 1.02% to 4.85%, and it needed a longer run time than BLAT. Further, we evaluated the intron information of 10 complete plant genomes. As non-coding sequences, intron lengths are not limited by a triplet codon frame; so, intron lengths have three phases: a multiple of three bases (3n), a multiple of three bases plus one (3n + 1), and a multiple of three bases plus two (3n + 2). It was widely accepted that the percentages of the 3n, 3n + 1, and 3n + 2 introns were quite similar in genomes. Our studies showed that 80% (8/10) of species were similar in terms of the number of three phases. The percentages of 3n introns in Ostreococcus lucimarinus was excessive (47.7%), while in Ostreococcus tauri, it was deficient (29.1%). This discrepancy could have been the result of errors in intron prediction. It is suggested that a three-phase evaluation is a fast and effective method of detecting intron annotation problems.

Keyword

intron length distributions; intron prediction; plant; three phases

MeSH Terms

Codon
Genome
Genome, Plant
Humans
Introns
Plants
Triplets
Codon