Analysis and prediction of gene splice sites in four Aspergillus genomes

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Analysis and prediction of gene splice sites in four Aspergillus genomes. / Wang, Kai; Ussery, David Wayne; Brunak, Søren.

In: Fungal Genetics and Biology, Vol. 46 Suppl 1, 2008, p. S14-8.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Wang, K, Ussery, DW & Brunak, S 2008, 'Analysis and prediction of gene splice sites in four Aspergillus genomes', Fungal Genetics and Biology, vol. 46 Suppl 1, pp. S14-8. https://doi.org/10.1016/j.fgb.2008.09.010

APA

Wang, K., Ussery, D. W., & Brunak, S. (2008). Analysis and prediction of gene splice sites in four Aspergillus genomes. Fungal Genetics and Biology, 46 Suppl 1, S14-8. https://doi.org/10.1016/j.fgb.2008.09.010

Vancouver

Wang K, Ussery DW, Brunak S. Analysis and prediction of gene splice sites in four Aspergillus genomes. Fungal Genetics and Biology. 2008;46 Suppl 1:S14-8. https://doi.org/10.1016/j.fgb.2008.09.010

Author

Wang, Kai ; Ussery, David Wayne ; Brunak, Søren. / Analysis and prediction of gene splice sites in four Aspergillus genomes. In: Fungal Genetics and Biology. 2008 ; Vol. 46 Suppl 1. pp. S14-8.

Bibtex

@article{158dddd03caa11df928f000ea68e967b,
title = "Analysis and prediction of gene splice sites in four Aspergillus genomes",
abstract = "Several Aspergillus fungal genomic sequences have been published, with many more in progress. Obviously, it is essential to have high-quality, consistently annotated sets of proteins from each of the genomes, in order to make meaningful comparisons. We have developed a dedicated, publicly available, splice site prediction program called NetAspGene, for the genus Aspergillus. Gene sequences from Aspergillus fumigatus, the most common mould pathogen, were used to build and test our model. Compared to many animals and plants, Aspergillus contains smaller introns; thus we have applied a larger window size on single local networks for training, to cover both donor and acceptor site information. We have applied NetAspGene to other Aspergilli, including Aspergillus nidulans, Aspergillus oryzae, and Aspergillus niger. Evaluation with independent data sets reveal that NetAspGene performs substantially better splice site prediction than other available tools. NetAspGene will be very helpful for the study in Aspergillus splice sites and especially in alternative splicing. A webpage for NetAspGene is publicly available at https://www.cbs.dtu.dk/services/NetAspGene.",
author = "Kai Wang and Ussery, {David Wayne} and S{\o}ren Brunak",
note = "Keywords: Aspergillus; Computational Biology; Genome, Fungal; RNA Splice Sites; Software",
year = "2008",
doi = "10.1016/j.fgb.2008.09.010",
language = "English",
volume = "46 Suppl 1",
pages = "S14--8",
journal = "Fungal Genetics and Biology",
issn = "1087-1845",
publisher = "Academic Press",

}

RIS

TY - JOUR

T1 - Analysis and prediction of gene splice sites in four Aspergillus genomes

AU - Wang, Kai

AU - Ussery, David Wayne

AU - Brunak, Søren

N1 - Keywords: Aspergillus; Computational Biology; Genome, Fungal; RNA Splice Sites; Software

PY - 2008

Y1 - 2008

N2 - Several Aspergillus fungal genomic sequences have been published, with many more in progress. Obviously, it is essential to have high-quality, consistently annotated sets of proteins from each of the genomes, in order to make meaningful comparisons. We have developed a dedicated, publicly available, splice site prediction program called NetAspGene, for the genus Aspergillus. Gene sequences from Aspergillus fumigatus, the most common mould pathogen, were used to build and test our model. Compared to many animals and plants, Aspergillus contains smaller introns; thus we have applied a larger window size on single local networks for training, to cover both donor and acceptor site information. We have applied NetAspGene to other Aspergilli, including Aspergillus nidulans, Aspergillus oryzae, and Aspergillus niger. Evaluation with independent data sets reveal that NetAspGene performs substantially better splice site prediction than other available tools. NetAspGene will be very helpful for the study in Aspergillus splice sites and especially in alternative splicing. A webpage for NetAspGene is publicly available at https://www.cbs.dtu.dk/services/NetAspGene.

AB - Several Aspergillus fungal genomic sequences have been published, with many more in progress. Obviously, it is essential to have high-quality, consistently annotated sets of proteins from each of the genomes, in order to make meaningful comparisons. We have developed a dedicated, publicly available, splice site prediction program called NetAspGene, for the genus Aspergillus. Gene sequences from Aspergillus fumigatus, the most common mould pathogen, were used to build and test our model. Compared to many animals and plants, Aspergillus contains smaller introns; thus we have applied a larger window size on single local networks for training, to cover both donor and acceptor site information. We have applied NetAspGene to other Aspergilli, including Aspergillus nidulans, Aspergillus oryzae, and Aspergillus niger. Evaluation with independent data sets reveal that NetAspGene performs substantially better splice site prediction than other available tools. NetAspGene will be very helpful for the study in Aspergillus splice sites and especially in alternative splicing. A webpage for NetAspGene is publicly available at https://www.cbs.dtu.dk/services/NetAspGene.

U2 - 10.1016/j.fgb.2008.09.010

DO - 10.1016/j.fgb.2008.09.010

M3 - Journal article

C2 - 18948220

VL - 46 Suppl 1

SP - S14-8

JO - Fungal Genetics and Biology

JF - Fungal Genetics and Biology

SN - 1087-1845

ER -

ID: 18947070