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Results: 1 to 20 of 137

1.

Gene identification in novel eukaryotic genomes by self-training algorithm.

Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M.

Nucleic Acids Res. 2005 Nov 28;33(20):6494-506. Print 2005.

PMID:
16314312
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.

Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M.

Genome Res. 2008 Dec;18(12):1979-90. doi: 10.1101/gr.081612.108. Epub 2008 Aug 29.

PMID:
18757608
[PubMed - indexed for MEDLINE]
Free PMC Article
3.
4.

SCGPred: a score-based method for gene structure prediction by combining multiple sources of evidence.

Li X, Ren Q, Weng Y, Cai H, Zhu Y, Zhang Y.

Genomics Proteomics Bioinformatics. 2008 Dec;6(3-4):175-85. doi: 10.1016/S1672-0229(09)60005-X.

PMID:
19329068
[PubMed - indexed for MEDLINE]
Free Article
5.

Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite.

Borodovsky M, Lomsadze A.

Curr Protoc Bioinformatics. 2011 Sep;Chapter 4:Unit 4.5.1-17. doi: 10.1002/0471250953.bi0405s35.

PMID:
21901741
[PubMed - indexed for MEDLINE]
6.

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes.

Zhu H, Hu GQ, Yang YF, Wang J, She ZS.

BMC Bioinformatics. 2007 Mar 16;8:97.

PMID:
17367537
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Ab initio gene identification in metagenomic sequences.

Zhu W, Lomsadze A, Borodovsky M.

Nucleic Acids Res. 2010 Jul;38(12):e132. doi: 10.1093/nar/gkq275. Epub 2010 Apr 19.

PMID:
20403810
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

Besemer J, Lomsadze A, Borodovsky M.

Nucleic Acids Res. 2001 Jun 15;29(12):2607-18.

PMID:
11410670
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome.

Christoffels A, Bartfai R, Srinivasan H, Komen H, Orban L.

BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S2.

PMID:
17254304
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite.

Borodovsky M, Lomsadze A.

Curr Protoc Microbiol. 2014 Feb 6;32:Unit 1E.7.. doi: 10.1002/9780471729259.mc01e07s32.

PMID:
24510847
[PubMed - in process]
11.

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.

Besemer J, Borodovsky M.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4.

PMID:
15980510
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Computational approaches to gene prediction.

Do JH, Choi DK.

J Microbiol. 2006 Apr;44(2):137-44. Review.

PMID:
16728949
[PubMed - indexed for MEDLINE]
Free Article
13.

Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes.

Shmatkov AM, Melikyan AA, Chernousko FL, Borodovsky M.

Bioinformatics. 1999 Nov;15(11):874-86.

PMID:
10743554
[PubMed - indexed for MEDLINE]
Free Article
14.

Self-identification of protein-coding regions in microbial genomes.

Audic S, Claverie JM.

Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):10026-31.

PMID:
9707594
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence.

Brejová B, Vinar T, Chen Y, Wang S, Zhao G, Brown DG, Li M, Zhou Y.

Nucleic Acids Res. 2009 Apr;37(7):e52. doi: 10.1093/nar/gkp052. Epub 2009 Mar 5.

PMID:
19264800
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Ab initio gene finding in Drosophila genomic DNA.

Salamov AA, Solovyev VV.

Genome Res. 2000 Apr;10(4):516-22.

PMID:
10779491
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

Arumugam M, Wei C, Brown RH, Brent MR.

Genome Biol. 2006;7 Suppl 1:S5.1-10. Epub 2006 Aug 7.

PMID:
16925839
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques.

Goodswen SJ, Kennedy PJ, Ellis JT.

PLoS One. 2012;7(11):e50609. doi: 10.1371/journal.pone.0050609. Epub 2012 Nov 30.

PMID:
23226328
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Gene prediction with a hidden Markov model and a new intron submodel.

Stanke M, Waack S.

Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25.

PMID:
14534192
[PubMed - indexed for MEDLINE]
Free Article
20.

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

Stanke M, Tzvetkova A, Morgenstern B.

Genome Biol. 2006;7 Suppl 1:S11.1-8. Epub 2006 Aug 7.

PMID:
16925833
[PubMed - indexed for MEDLINE]
Free PMC Article

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