References
- Purdom E, Simpson KM, Robinson MD, Conboy JG, Lapuk AV, Speed TP. FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics 2008;24:1707-1714. https://doi.org/10.1093/bioinformatics/btn284
- Zhou L, Pertea M, Delcher AL, Florea L. Sim4cc: a cross-species spliced alignment program. Nucleic Acids Res 2009;37:e80. https://doi.org/10.1093/nar/gkp319
- Harrington ED, Bork P. Sircah: a tool for the detection and visualization of alternative transcripts. Bioinformatics 2008;24:1959-1960. https://doi.org/10.1093/bioinformatics/btn361
- Rambaldi D, Felice B, Praz V, Bucher P, Cittaro D, Guffanti A. Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. BMC Bioinformatics 2007;8 Suppl 1:S17. https://doi.org/10.1186/1471-2105-8-S1-S17
- Mitchell RA, Castells-Brooke N, Taubert J, Verrier PJ, Leader DJ, Rawlings CJ. Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence. Nucleic Acids Res 2007;35:W148-W151. https://doi.org/10.1093/nar/gkm220
- Lazzarato F, Franceschinis G, Botta M, Cordero F, Calogero RA. RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets. Bioinformatics 2004;20:2848-2850. https://doi.org/10.1093/bioinformatics/bth287
- Milanesi L, Rogozin IB. ESTMAP: a system for expressed sequence tags mapping on genomic sequences. IEEE Trans Nanobioscience 2003;2:75-78. https://doi.org/10.1109/TNB.2003.813928
- Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 2010;38:e178. https://doi.org/10.1093/nar/gkq622
- Dimon MT, Sorber K, DeRisi JL. HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PLoS One 2010;5:e13875. https://doi.org/10.1371/journal.pone.0013875
- Foissac S, Bardou P, Moisan A, Cros MJ, Schiex T. EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences. Nucleic Acids Res 2003;31:3742-3745. https://doi.org/10.1093/nar/gkg586
- Kent WJ. BLAT: the BLAST-like alignment tool. Genome Res 2002;12:656-664.
- Lee C, Atanelov L, Modrek B, Xing Y. ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res 2003;31:101-105. https://doi.org/10.1093/nar/gkg029
- Odenwald WF, Rasband W, Kuzin A, Brody T. EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA. Proc Natl Acad Sci U S A 2005;102:14700-14705. https://doi.org/10.1073/pnas.0506915102
- Castrignano T, De Meo PD, Grillo G, Liuni S, Mignone F, Talamo IG, et al. GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags. Bioinformatics 2006;22:497-499. https://doi.org/10.1093/bioinformatics/bti754
- Tamaki S, Arakawa K, Kono N, Tomita M. Restauro-G: a rapid genome re-annotation system for comparative genomics. Genomics Proteomics Bioinformatics 2007;5:53-58. https://doi.org/10.1016/S1672-0229(07)60014-X
- Kent WJ, Zahler AM. The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans . Nucleic Acids Res 2000;28:91-93. https://doi.org/10.1093/nar/28.1.91
- Irimia M, Roy SW. Spliceosomal introns as tools for genomic and evolutionary analysis. Nucleic Acids Res 2008;36:1703-1712. https://doi.org/10.1093/nar/gkn012
- Roy SW, Penny D. Intron length distributions and gene prediction. Nucleic Acids Res 2007;35:4737-4742. https://doi.org/10.1093/nar/gkm281
- Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia- Hernandez M, Foerster H, et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 2008;36:D1009-D1014.
- Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica ). Science 2002;296:92-100. https://doi.org/10.1126/science.1068275
- Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica) . Science 2002;296:79-92. https://doi.org/10.1126/science.1068037
- Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009;326:1112-1115. https://doi.org/10.1126/science.1178534
- Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, et al. The Sorghum bicolor genome and the diversification of grasses. Nature 2009;457:551-556. https://doi.org/10.1038/nature07723
- Han YH, Zhang ZH, Liu JH, Lu JY, Huang SW, Jin WW. Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis sativus L.) by fluorescence in situ hybridization. Cytogenet Genome Res 2008;122:80-88. https://doi.org/10.1159/000151320
- Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007;318:245-250. https://doi.org/10.1126/science.1143609
- Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A 2007;104:7705-7710. https://doi.org/10.1073/pnas.0611046104
- Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, et al. Sequencing the genespaces of Medicago truncatula and Lotus japonicus . Plant Physiol 2005;137:1174-1181. https://doi.org/10.1104/pp.104.057034
- Lanier W, Moustafa A, Bhattacharya D, Comeron JM. EST analysis of Ostreococcus lucimarinus , the most compact eukaryotic genome, shows an excess of introns in highly expressed genes. PLoS One 2008;3:e2171. https://doi.org/10.1371/journal.pone.0002171
- Derelle E, Ferraz C, Rombauts S, Rouze P, Worden AZ, Robbens S, et al. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A 2006;103: 11647-11652. https://doi.org/10.1073/pnas.0604795103