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ParsEval: parallel comparison and analysis of gene structure annotations.
Standage DS, Brendel VP. Standage DS, et al. BMC Bioinformatics. 2012 Aug 1;13:187. doi: 10.1186/1471-2105-13-187. BMC Bioinformatics. 2012. PMID: 22852583 Free PMC article.
Multi-query sequence BLAST output examination with MuSeqBox.
Xing L, Brendel V. Xing L, et al. Bioinformatics. 2001 Aug;17(8):744-5. doi: 10.1093/bioinformatics/17.8.744. Bioinformatics. 2001. PMID: 11524378
Optimal spliced alignment of homologous cDNA to a genomic DNA template.
Usuka J, Zhu W, Brendel V. Usuka J, et al. Bioinformatics. 2000 Mar;16(3):203-11. doi: 10.1093/bioinformatics/16.3.203. Bioinformatics. 2000. PMID: 10869013
MaizeGDB becomes 'sequence-centric'.
Sen TZ, Andorf CM, Schaeffer ML, Harper LC, Sparks ME, Duvick J, Brendel VP, Cannon E, Campbell DA, Lawrence CJ. Sen TZ, et al. Database (Oxford). 2009;2009:bap020. doi: 10.1093/database/bap020. Epub 2009 Dec 7. Database (Oxford). 2009. PMID: 21847242 Free PMC article.
Gene Structure Annotation at PlantGDB.
Brendel V. Brendel V. Methods Mol Biol. 2007;406:521-33. doi: 10.1007/978-1-59745-535-0_25. Methods Mol Biol. 2007. PMID: 18287710
PlantGDB: a resource for comparative plant genomics.
Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V. Duvick J, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D959-65. doi: 10.1093/nar/gkm1041. Epub 2007 Dec 6. Nucleic Acids Res. 2008. PMID: 18063570 Free PMC article.
Tracembler--software for in-silico chromosome walking in unassembled genomes.
Dong Q, Wilkerson MD, Brendel V. Dong Q, et al. BMC Bioinformatics. 2007 May 9;8:151. doi: 10.1186/1471-2105-8-151. BMC Bioinformatics. 2007. PMID: 17490482 Free PMC article.
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