An overview of the current status of eukaryote gene prediction strategies.

As sequence data continues to be generated at a logarithmic rate our dependence on effective in silico gene prediction methods is also increasing. Herein, I review the current state of eukaryote gene prediction methods; their strengths, weaknesses and future directions.

[1]  J. Do,et al.  Computational approaches to gene prediction. , 2006, Journal of microbiology.

[2]  M. Kozak,et al.  Interpreting cDNA sequences: Some insights from studies on translation , 1996, Mammalian Genome.

[3]  M. Ashburner,et al.  Annotating eukaryote genomes. , 2000, Current opinion in structural biology.

[4]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[5]  M. Brent.  How does eukaryotic gene prediction work? , 2007, Nature Biotechnology.

[6]  J. Micol,et al.  OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana , 1999, FEBS letters.

[7]  Jonathan E. Allen,et al.  Computational gene prediction using multiple sources of evidence. , 2003, Genome research.

[8]  J. Mattick,et al.  Non‐coding RNAs: regulators of disease , 2010, The Journal of pathology.

[9]  Stefan Stamm,et al.  Regulation of Alternative Splicing by Reversible Protein Phosphorylation* , 2008, Journal of Biological Chemistry.

[10]  T. Blumenthal.  Gene clusters and polycistronic transcription in eukaryotes , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[11]  Martin Reczko,et al.  MicroRNAs and Cancer—The Search Begins! , 2009, IEEE Transactions on Information Technology in Biomedicine.

[12]  P. Rouzé,et al.  Current methods of gene prediction, their strengths and weaknesses. , 2002, Nucleic acids research.

[13]  M. Brent,et al.  Recent advances in gene structure prediction. , 2004, Current opinion in structural biology.

[14]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[15]  Paul Flicek,et al.  Gene prediction: compare and CONTRAST , 2007, Genome Biology.

[16]  C. Burge,et al.  Computational inference of homologous gene structures in the human genome. , 2001, Genome research.

[17]  Piero Carninci,et al.  Annotating non-coding transcription using functional genomics strategies. , 2009, Briefings in functional genomics & proteomics.

[18]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[19]  P. Bork,et al.  Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions? , 2008, BMC Genomics.

[20]  Roy D Sleator,et al.  The human superorganism - of microbes and men. , 2010, Medical hypotheses.

[21]  Koby Crammer,et al.  Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction , 2007, PLoS Comput. Biol..

[22]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[23]  Jon D. McAuliffe,et al.  Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome , 2003, Science.

[24]  A. MacMillan,et al.  Pre-mRNA splicing: a complex picture in higher definition. , 2008, Trends in biochemical sciences.

[25]  Axel Mosig,et al.  Customized strategies for discovering distant ncRNA homologs. , 2009, Briefings in functional genomics & proteomics.

[26]  Qizhi Yao,et al.  MicroRNAs: Control and Loss of Control in Human Physiology and Disease , 2009, World Journal of Surgery.

[27]  M. Brent,et al.  Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. , 2003, Genome research.

[28]  J. Claverie.  Computational methods for the identification of genes in vertebrate genomic sequences. , 1997, Human molecular genetics.

[29]  R. Guigó,et al.  An assessment of gene prediction accuracy in large DNA sequences. , 2000, Genome research.