Cargando…

Intron length distributions and gene prediction

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 nu...

Descripción completa

Detalles Bibliográficos
Autores principales: Roy, Scott William, Penny, David
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950532/
https://www.ncbi.nlm.nih.gov/pubmed/17617639
http://dx.doi.org/10.1093/nar/gkm281
_version_ 1782134557136388096
author Roy, Scott William
Penny, David
author_facet Roy, Scott William
Penny, David
author_sort Roy, Scott William
collection PubMed
description 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.
format Text
id pubmed-1950532
institution National Center for Biotechnology Information
language English
publishDate 2007
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-19505322007-08-22 Intron length distributions and gene prediction Roy, Scott William Penny, David Nucleic Acids Res Genomics 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. Oxford University Press 2007-07 2007-07-07 /pmc/articles/PMC1950532/ /pubmed/17617639 http://dx.doi.org/10.1093/nar/gkm281 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Genomics
Roy, Scott William
Penny, David
Intron length distributions and gene prediction
title Intron length distributions and gene prediction
title_full Intron length distributions and gene prediction
title_fullStr Intron length distributions and gene prediction
title_full_unstemmed Intron length distributions and gene prediction
title_short Intron length distributions and gene prediction
title_sort intron length distributions and gene prediction
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950532/
https://www.ncbi.nlm.nih.gov/pubmed/17617639
http://dx.doi.org/10.1093/nar/gkm281
work_keys_str_mv AT royscottwilliam intronlengthdistributionsandgeneprediction
AT pennydavid intronlengthdistributionsandgeneprediction