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For: Usuka J, Brendel V. Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring. J Mol Biol 2000;297:1075-85. [PMID: 10764574 DOI: 10.1006/jmbi.2000.3641] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Number Cited by Other Article(s)
1
Li H. Protein-to-genome alignment with miniprot. Bioinformatics 2023;39:btad014. [PMID: 36648328 PMCID: PMC9869432 DOI: 10.1093/bioinformatics/btad014] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/25/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023]  Open
2
König S, Romoth L, Stanke M. Comparative Genome Annotation. Methods Mol Biol 2018;1704:189-212. [PMID: 29277866 DOI: 10.1007/978-1-4939-7463-4_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
3
A Comprehensive Review of Emerging Computational Methods for Gene Identification. JOURNAL OF INFORMATION PROCESSING SYSTEMS 2016. [DOI: 10.3745/jips.04.0023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
4
Differential pre-mRNA Splicing Alters the Transcript Diversity of Helitrons Between the Maize Inbred Lines. G3-GENES GENOMES GENETICS 2015;5:1703-11. [PMID: 26070844 PMCID: PMC4528327 DOI: 10.1534/g3.115.018630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
5
Rauch HB, Patrick TL, Klusman KM, Battistuzzi FU, Mei W, Brendel VP, Lal SK. Discovery and expression analysis of alternative splicing events conserved among plant SR proteins. Mol Biol Evol 2013;31:605-13. [PMID: 24356560 DOI: 10.1093/molbev/mst238] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
6
Molecular characterization of the chalcone isomerase gene family in Deschampsia antarctica. Polar Biol 2013. [DOI: 10.1007/s00300-013-1346-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
7
Gene capture by Helitron transposons reshuffles the transcriptome of maize. Genetics 2011;190:965-75. [PMID: 22174072 PMCID: PMC3296258 DOI: 10.1534/genetics.111.136176] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
8
Inagaki YS, Etherington G, Geisler K, Field B, Dokarry M, Ikeda K, Mutsukado Y, Dicks J, Osbourn A. Investigation of the potential for triterpene synthesis in rice through genome mining and metabolic engineering. THE NEW PHYTOLOGIST 2011;191:432-448. [PMID: 21501172 DOI: 10.1111/j.1469-8137.2011.03712.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
9
Ahmed F, Benedito VA, Zhao PX. Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives. FRONTIERS IN PLANT SCIENCE 2011;2:84. [PMID: 22639614 PMCID: PMC3355573 DOI: 10.3389/fpls.2011.00084] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/03/2011] [Indexed: 05/03/2023]
10
Picardi E, Pesole G. Computational methods for ab initio and comparative gene finding. Methods Mol Biol 2010;609:269-84. [PMID: 20221925 DOI: 10.1007/978-1-60327-241-4_16] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
11
Labate JA, Robertson LD, Wu F, Tanksley SD, Baldo AM. EST, COSII, and arbitrary gene markers give similar estimates of nucleotide diversity in cultivated tomato (Solanum lycopersicum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009;118:1005-14. [PMID: 19153710 DOI: 10.1007/s00122-008-0957-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 12/20/2008] [Indexed: 05/13/2023]
12
Gotoh O. Direct mapping and alignment of protein sequences onto genomic sequence. ACTA ACUST UNITED AC 2008;24:2438-44. [PMID: 18728043 DOI: 10.1093/bioinformatics/btn460] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
13
Tasma IM, Brendel V, Whitham SA, Bhattacharyya MK. Expression and evolution of the phosphoinositide-specific phospholipase C gene family in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008;46:627-637. [PMID: 18534862 DOI: 10.1016/j.plaphy.2008.04.015] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2007] [Indexed: 05/04/2023]
14
Vergara IA, Norambuena T, Ferrada E, Slater AW, Melo F. StAR: a simple tool for the statistical comparison of ROC curves. BMC Bioinformatics 2008;9:265. [PMID: 18534022 PMCID: PMC2435548 DOI: 10.1186/1471-2105-9-265] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 06/05/2008] [Indexed: 02/08/2023]  Open
15
Jameson N, Georgelis N, Fouladbash E, Martens S, Hannah LC, Lal S. Helitron mediated amplification of cytochrome P450 monooxygenase gene in maize. PLANT MOLECULAR BIOLOGY 2008;67:295-304. [PMID: 18327644 DOI: 10.1007/s11103-008-9318-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 02/22/2008] [Indexed: 05/13/2023]
16
Gupta S, Ciungu A, Jameson N, Lal SK. Alternative splicing expression of U1 snRNP 70K gene is evolutionary conserved between different plant species. ACTA ACUST UNITED AC 2007;17:254-61. [PMID: 17312944 DOI: 10.1080/10425170600856642] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
17
Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V. Comparative plant genomics resources at PlantGDB. PLANT PHYSIOLOGY 2005;139:610-8. [PMID: 16219921 PMCID: PMC1255980 DOI: 10.1104/pp.104.059212] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Revised: 05/04/2005] [Accepted: 05/12/2005] [Indexed: 05/04/2023]
18
Dong Q, Kroiss L, Oakley FD, Wang BB, Brendel V. Comparative EST analyses in plant systems. Methods Enzymol 2005;395:400-18. [PMID: 15984049 DOI: 10.1016/s0076-6879(05)95022-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
19
Yao H, Guo L, Fu Y, Borsuk LA, Wen TJ, Skibbe DS, Cui X, Scheffler BE, Cao J, Emrich SJ, Ashlock DA, Schnable PS. Evaluation of five ab initio gene prediction programs for the discovery of maize genes. PLANT MOLECULAR BIOLOGY 2005;57:445-60. [PMID: 15830133 DOI: 10.1007/s11103-005-0271-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 01/06/2005] [Indexed: 05/20/2023]
20
Gupta S, Gallavotti A, Stryker GA, Schmidt RJ, Lal SK. A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes. PLANT MOLECULAR BIOLOGY 2005;57:115-27. [PMID: 15821872 DOI: 10.1007/s11103-004-6636-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Revised: 11/27/2004] [Indexed: 05/08/2023]
21
Degroeve S, Saeys Y, De Baets B, Rouzé P, Van de Peer Y. SpliceMachine: predicting splice sites from high-dimensional local context representations. Bioinformatics 2004;21:1332-8. [PMID: 15564294 DOI: 10.1093/bioinformatics/bti166] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
22
Li LH, Li JC, Lin YF, Lin CY, Chen CY, Tsai SF. Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping. Nucleic Acids Res 2004;32:e27. [PMID: 14960710 PMCID: PMC373421 DOI: 10.1093/nar/gnh025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
23
Zhu W, Schlueter SD, Brendel V. Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping. PLANT PHYSIOLOGY 2003;132:469-84. [PMID: 12805580 PMCID: PMC166990 DOI: 10.1104/pp.102.018101] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2002] [Revised: 01/06/2003] [Accepted: 02/20/2003] [Indexed: 05/18/2023]
24
Schoof H, Karlowski WM. Comparison of rice and Arabidopsis annotation. CURRENT OPINION IN PLANT BIOLOGY 2003;6:106-112. [PMID: 12667865 DOI: 10.1016/s1369-5266(03)00003-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
25
Zhang W, Wang Y, Long J, Girton J, Johansen J, Johansen KM. A developmentally regulated splice variant from the complex lola locus encoding multiple different zinc finger domain proteins interacts with the chromosomal kinase JIL-1. J Biol Chem 2003;278:11696-704. [PMID: 12538650 DOI: 10.1074/jbc.m213269200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
26
Pachter L, Alexandersson M, Cawley S. Applications of generalized pair hidden Markov models to alignment and gene finding problems. J Comput Biol 2002;9:389-99. [PMID: 12015888 DOI: 10.1089/10665270252935520] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
27
Mathé C, Sagot MF, Schiex T, Rouzé P. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res 2002;30:4103-17. [PMID: 12364589 PMCID: PMC140543 DOI: 10.1093/nar/gkf543] [Citation(s) in RCA: 209] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2002] [Revised: 08/07/2002] [Accepted: 08/07/2002] [Indexed: 11/14/2022]  Open
28
Brendel V, Kurtz S, Walbot V. Comparative genomics of Arabidopsis and maize: prospects and limitations. Genome Biol 2002;3:REVIEWS1005. [PMID: 11897028 PMCID: PMC139024 DOI: 10.1186/gb-2002-3-3-reviews1005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
29
Claverie JM, Abergel C, Audic S, Ogata H. Recent advances in computational genomics. Pharmacogenomics 2001;2:361-72. [PMID: 11722286 DOI: 10.1517/14622416.2.4.361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]  Open
30
Cho Y, Walbot V. Computational methods for gene annotation: the Arabidopsis genome. Curr Opin Biotechnol 2001;12:126-30. [PMID: 11287224 DOI: 10.1016/s0958-1669(00)00185-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
31
Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O, Zhang MQ. An alternative-exon database and its statistical analysis. DNA Cell Biol 2000;19:739-56. [PMID: 11177572 DOI: 10.1089/104454900750058107] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
32
Current awareness on comparative and functional genomics. Yeast 2000;17:339-46. [PMID: 11119313 PMCID: PMC2448380 DOI: 10.1002/1097-0061(200012)17:4<339::aid-yea10>3.0.co;2-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]  Open
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