- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Recently Accepted Articles ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 502827, 11 pages
ASPic-GeneID: A Lightweight Pipeline for Gene Prediction and Alternative Isoforms Detection
1Centre Nacional d’Anàlisi Genòmica (CNAG), Parc Científic de Barcelona, 08028 Barcelona, Spain
2Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, 70126 Bari, Italy
3Istituto di Biomembrane e Bioenergetica del Consiglio Nazionale delle Ricerche (CNR), 70126 Bari, Italy
4Centre de Regulació Genòmica (CRG), 08003 Barcelona, Spain
5Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
6Centro di Eccellenza in Genomica Comparata, Università degli Studi di Bari, 70126 Bari, Italy
Received 16 June 2013; Revised 1 August 2013; Accepted 4 August 2013
Academic Editor: Tao Huang
Copyright © 2013 Tyler Alioto et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- J. Zhang, R. Chiodini, A. Badr, and G. Zhang, “The impact of next-generation sequencing on genomics,” Journal of Genetics and Genomics, vol. 38, no. 3, pp. 95–109, 2011.
- E. Picardi and G. Pesole, “Computational methods for ab initio and comparative gene finding,” Methods in Molecular Biology, vol. 609, pp. 269–284, 2010.
- T. Alioto, “Gene prediction,” Methods in Molecular Biology, vol. 855, pp. 175–201, 2012.
- I. Korf, “Gene finding in novel genomes,” BMC Bioinformatics, vol. 5, article 59, 2004.
- M. Stanke, R. Steinkamp, S. Waack, and B. Morgenstern, “AUGUSTUS: a web server for gene finding in eukaryotes,” Nucleic Acids Research, vol. 32, pp. W309–W312, 2004.
- S. L. Cawley and L. Pachter, “HMM sampling and applications to gene finding and alternative splicing,” Bioinformatics, vol. 19, supplement 2, pp. ii36–ii41, 2003.
- J. S. Pedersen and J. Hein, “Gene finding with a hidden Markov model of genome structure and evolution,” Bioinformatics, vol. 19, no. 2, pp. 219–227, 2003.
- R. Guigó, P. Flicek, J. F. Abril et al., “EGASP: the human ENCODE Genome Annotation Assessment Project,” Genome Biology, vol. 7, supplement 1, pp. S2.1–S2.31, 2006.
- C. Wei and M. R. Brent, “Using ESTs to improve the accuracy of de novo gene prediction,” BMC Bioinformatics, vol. 7, article 327, 2006.
- G. Parra, P. Agarwal, J. F. Abril, T. Wiehe, J. W. Fickett, and R. Guigó, “Comparative gene prediction in human and mouse,” Genome Research, vol. 13, no. 1, pp. 108–117, 2003.
- M. J. van Baren, B. C. Koebbe, and M. R. Brent, “Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences,” in Current Protocols in Bioinformatics, A. D. Baxevanis, Ed., chapter 4, unit 4.8, 2007.
- S. S. Gross, C. B. Do, M. Sirota, and S. Batzoglou, “CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction,” Genome Biology, vol. 8, no. 12, article R269, 2007.
- O. Jaillon, J.-M. Aury, B. Noel et al., “The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla,” Nature, vol. 449, no. 7161, pp. 463–467, 2007.
- “Analysis of the genome sequence of the flowering plant Arabidopsis thaliana,” Nature, vol. 408, no. 6814, pp. 796–815, 2000.
- G. A. Tuskan, S. DiFazio, S. Jansson et al., “The genome of black cottonwood, Populus trichocarpa (Torr. & Gray),” Science, vol. 313, no. 5793, pp. 1596–1604, 2006.
- The Tomato Genome Consortium, “The tomato genome sequence provides insights into fleshy fruit evolution,” Nature, vol. 485, no. 7400, pp. 635–641, 2012.
- R. Guigó and M. G. Reese, “EGASP: collaboration through competition to find human genes,” Nature Methods, vol. 2, no. 8, pp. 575–577, 2005.
- N. de Souza, “The ENCODE project,” Nature Methods, vol. 9, no. 11, article 1046, 2012.
- L. L. Elnitski, P. Shah, R. T. Moreland, L. Umayam, T. G. Wolfsberg, and A. D. Baxevanis, “The ENCODEdb portal: simplified access to ENCODE consortium data,” Genome Research, vol. 17, no. 6, pp. 954–959, 2007.
- J. Harrow, F. Denoeud, A. Frankish et al., “GENCODE: producing a reference annotation for ENCODE,” Genome Biology, vol. 7, supplement 1, pp. S4.1–S4.9, 2006.
- S. H. Nagaraj, R. B. Gasser, and S. Ranganathan, “A hitchhiker's guide to Expressed Sequence Tag (EST) analysis,” Briefings in Bioinformatics, vol. 8, no. 1, pp. 6–21, 2007.
- M. Stanke, A. Tzvetkova, and B. Morgenstern, “AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome,” Genome Biology, vol. 7, supplement 1, pp. S11.1–S11.8, 2006.
- A. Krogh, “Using database matches with HMMGene for automated gene detection in Drosophila,” Genome Research, vol. 10, no. 4, pp. 523–528, 2000.
- M. Arumugam, C. Wei, R. H. Brown, and M. R. Brent, “Pairagon+N-SCAN_EST: a model-based gene annotation pipeline,” Genome Biology, vol. 7, supplement 1, pp. S5.1–S5.10, 2006.
- S. Djebali, F. Delaplace, and H. R. Crollius, “Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA,” Genome Biology, vol. 7, supplement 1, pp. S7.1–S7.10, 2006.
- T. Castrignanò, R. Rizzi, I. G. Talamo et al., “ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization,” Nucleic Acids Research, vol. 34, pp. W440–W443, 2006.
- P. Bonizzoni, R. Rizzi, and G. Pesole, “ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences,” BMC Bioinformatics, vol. 6, article 244, 2005.
- E. Blanco, G. Parra, and R. Guigo, “Using geneid to identify genes,” in Current Protocols in Bioinformatics, A. D. Baxevanis, Ed., chapter 4, unit 4.3, 2007.
- G. Parra, E. Blanco, and R. Guigó, “GeneId in Drosophila,” Genome Research, vol. 10, no. 4, pp. 511–515, 2000.
- T. D. Wu and C. K. Watanabe, “GMAP: a genomic mapping and alignment program for mRNA and EST sequences,” Bioinformatics, vol. 21, no. 9, pp. 1859–1875, 2005.
- W. J. Kent, “BLAT—the BLAST-like alignment tool,” Genome Research, vol. 12, no. 4, pp. 656–664, 2002.
- G. format, http://www.sanger.ac.uk/Software/formats/GFF/.
- S. M. J. Searle, J. Gilbert, V. Iyer, and M. Clamp, “The Otter annotation system,” Genome Research, vol. 14, no. 5, pp. 963–970, 2004.
- M. Burset and R. Guigó, “Evaluation of gene structure prediction programs,” Genomics, vol. 34, no. 3, pp. 353–367, 1996.
- S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990.
- A. Coghlan and R. Durbin, “Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure,” Bioinformatics, vol. 23, no. 12, pp. 1468–1475, 2007.
- S. W. Roy and D. Penny, “Intron length distributions and gene prediction,” Nucleic Acids Research, vol. 35, no. 14, pp. 4737–4742, 2007.
- D. V. Lu, R. H. Brown, M. Arumugam, and M. R. Brent, “Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner,” Bioinformatics, vol. 25, no. 13, pp. 1587–1593, 2009.
- D. S. Gerhard, “The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC),” Genome Research, vol. 14, no. 10, pp. 2121–2127, 2004.
- V. Solovyev, P. Kosarev, I. Seledsov, and D. Vorobyev, “Automatic annotation of eukaryotic genes, pseudogenes and promoters,” Genome Biology, vol. 7, pp. S10.11–S10.12, 2006.
- V. Curwen, E. Eyras, T. D. Andrews et al., “The Ensembl automatic gene annotation system,” Genome Research, vol. 14, no. 5, pp. 942–950, 2004.
- A. A. Salamov and V. V. Solovyev, “Ab initio gene finding in Drosophila genomic DNA,” Genome Research, vol. 10, no. 4, pp. 516–522, 2000.
- J. Q. Wu, D. Shteynberg, M. Arumugam, R. A. Gibbs, and M. R. Bren, “Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing,” Genome Research, vol. 14, no. 4, pp. 665–671, 2004.
- D. Weissglas-Volkov, C. L. Plaisier, A. Huertas-Vazquez et al., “Identification of two common variants contributing to serum apolipoprotein B levels in mexicans,” Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 30, no. 2, pp. 353–359, 2010.
- J. Besemer and M. Borodovsky, “GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses,” Nucleic Acids Research, vol. 33, no. 2, pp. W451–W454, 2005.
- B. Brejová, D. G. Brown, M. Li, and T. Vinař, “ExonHunter: a comprehensive approach to gene finding,” Bioinformatics, vol. 21, supplement 1, pp. i57–i65, 2005.
- M. L. Metzker, “Sequencing technologies the next generation,” Nature Reviews Genetics, vol. 11, no. 1, pp. 31–46, 2010.
- E. R. Mardis, “The impact of next-generation sequencing technology on genetics,” Trends in Genetics, vol. 24, no. 3, pp. 133–141, 2008.
- C. Trapnell, A. Roberts, L. Goff et al., “Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks,” Nature Protocols, vol. 7, no. 3, pp. 562–578, 2012.