Nucleic Acids Research Advance Access originally published online on July 7, 2007
Nucleic Acids Research 2007 35(14):4737-4742; doi:10.1093/nar/gkm281
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Nucleic Acids Research, 2007, Vol. 35, No. 14 4737-4742
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Genomics |
Intron length distributions and gene prediction
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
*To whom correspondence should be addressed. Tel: +64-6-350-5515. Ext. 7626; Fax: +64-6-350-5626; Email: scottwroy{at}gmail.com
Received February 7, 2007. Revised March 21, 2007. Accepted April 11, 2007.
Accurate gene prediction in eukaryotes is a difficult and subtle problem. Here we point out a useful feature of expected distributions of spliceosomal intron lengths. Since introns are removed from transcripts prior to translation, intron lengths are not expected to respect coding frame, thus the number of genomic introns that are a multiple of three bases (‘3n introns’) should be similar to the number that are a multiple of three plus one bases (or plus two bases). Skewed predicted intron length distributions thus suggest systematic errors in intron prediction. For instance, a genome-wide excess of 3n introns suggests that many internal exonic sequences have been incorrectly called introns, whereas a deficit of 3n introns suggests that many 3n introns that lack stop codons have been mistaken for exonic sequence. A survey of genomic annotations for 29 diverse eukaryotic species showed that skew in intron length distributions is a common problem. We discuss several examples of skews in genome-wide intron length distributions that indicate systematic problems with gene prediction. We suggest that evaluation of length distributions of predicted introns is a fast and simple method for detecting a variety of possible systematic biases in gene prediction or even problems with genome assemblies, and discuss ways in which these insights could be incorporated into genome annotation protocols.
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  M. Irimia and S. W. Roy Spliceosomal introns as tools for genomic and evolutionary analysis Nucleic Acids Res., March 1, 2008; 36(5): 1703 - 1712. [Abstract] [Full Text] [PDF]
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