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GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.
Besemer J, Borodovsky M. Besemer J, et al. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4. doi: 10.1093/nar/gki487. Nucleic Acids Res. 2005. PMID: 15980510 Free PMC article.
NCBI prokaryotic genome annotation pipeline.
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. Tatusova T, et al. Among authors: borodovsky m. Nucleic Acids Res. 2016 Aug 19;44(14):6614-24. doi: 10.1093/nar/gkw569. Epub 2016 Jun 24. Nucleic Acids Res. 2016. PMID: 27342282 Free PMC article.
UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing.
Burns PD, Li Y, Ma J, Borodovsky M. Burns PD, et al. Nucleic Acids Res. 2014 Feb;42(4):e25. doi: 10.1093/nar/gkt1141. Epub 2013 Nov 19. Nucleic Acids Res. 2014. PMID: 24259430 Free PMC article.
Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES.
Borodovsky M, Lomsadze A. Borodovsky M, et al. Curr Protoc Bioinformatics. 2011 Sep;Chapter 4:Unit 4.6.1-10. doi: 10.1002/0471250953.bi0406s35. Curr Protoc Bioinformatics. 2011. PMID: 21901742 Free PMC article.
Ab initio gene identification in metagenomic sequences.
Zhu W, Lomsadze A, Borodovsky M. Zhu W, et al. Nucleic Acids Res. 2010 Jul;38(12):e132. doi: 10.1093/nar/gkq275. Epub 2010 Apr 19. Nucleic Acids Res. 2010. PMID: 20403810 Free PMC article.
Prokaryotic gene prediction using GeneMark and GeneMark.hmm.
Borodovsky M, Mills R, Besemer J, Lomsadze A. Borodovsky M, et al. Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.5. doi: 10.1002/0471250953.bi0405s01. Curr Protoc Bioinformatics. 2003. PMID: 18428700
Evaluating the protein coding potential of exonized transposable element sequences.
Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK. Piriyapongsa J, et al. Biol Direct. 2007 Nov 26;2:31. doi: 10.1186/1745-6150-2-31. Biol Direct. 2007. PMID: 18036258 Free PMC article.
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