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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.
Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. ...Also, we show that as a result of application of the new method, several thousands of new genes could be added to existing annota …
Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. …
Improving gene annotation of complete viral genomes.
Mills R, Rozanov M, Lomsadze A, Tatusova T, Borodovsky M. Mills R, et al. Nucleic Acids Res. 2003 Dec 1;31(23):7041-55. doi: 10.1093/nar/gkg878. Nucleic Acids Res. 2003. PMID: 14627837 Free PMC article.
For example, a new gene predicted in the genome of the Epstein-Barr virus was shown to encode a protein similar to alpha-herpesvirus minor tegument protein UL14 with heat shock functions. ...In another example, several iterations of PSI-BLAST were required to demons …
For example, a new gene predicted in the genome of the Epstein-Barr virus was shown to encode a protein similar to alpha-herpe …
Gene identification in novel eukaryotic genomes by self-training algorithm.
Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M. Lomsadze A, et al. Nucleic Acids Res. 2005 Nov 28;33(20):6494-506. doi: 10.1093/nar/gki937. Print 2005. Nucleic Acids Res. 2005. PMID: 16314312 Free PMC article.
However, genomic organization of novel eukaryotic genomes is diverse and ab initio gene finding tools tuned up for previously studied species are rarely suitable for efficacious gene hunting in DNA sequences of a new genome. ...Thus, a self-training algorithm that h …
However, genomic organization of novel eukaryotic genomes is diverse and ab initio gene finding tools tuned up for previously studied specie …
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.
Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. Ter-Hovhannisyan V, et al. Genome Res. 2008 Dec;18(12):1979-90. doi: 10.1101/gr.081612.108. Epub 2008 Aug 29. Genome Res. 2008. PMID: 18757608 Free PMC article.
We describe a new ab initio algorithm, GeneMark-ES version 2, that identifies protein-coding genes in fungal genomes. The algorithm does not require a predetermined training set to estimate parameters of the underlying hidden Markov model (HMM). ...By eliminating th …
We describe a new ab initio algorithm, GeneMark-ES version 2, that identifies protein-coding genes in fungal genomes. The algorithm d …
Frameshift detection in prokaryotic genomic sequences.
Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M. Kislyuk A, et al. Int J Bioinform Res Appl. 2009;5(4):458-77. doi: 10.1504/IJBRA.2009.027519. Int J Bioinform Res Appl. 2009. PMID: 19640832
We have developed a new method for frameshift detection, a combination of ab initio and alignment-based algorithms, that can serve as a useful tool for sequencing quality control in the next generation sequencing. ...
We have developed a new method for frameshift detection, a combination of ab initio and alignment-based algorithms, that can s …
Identification of protein coding regions in RNA transcripts.
Tang S, Lomsadze A, Borodovsky M. Tang S, et al. Among authors: lomsadze a. Nucleic Acids Res. 2015 Jul 13;43(12):e78. doi: 10.1093/nar/gkv227. Epub 2015 Apr 13. Nucleic Acids Res. 2015. PMID: 25870408 Free PMC article.
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. Hoff KJ, et al. Among authors: lomsadze a. Bioinformatics. 2016 Mar 1;32(5):767-9. doi: 10.1093/bioinformatics/btv661. Epub 2015 Nov 11. Bioinformatics. 2016. PMID: 26559507 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: lomsadze a. 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.
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