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Approaches to Fungal Genome Annotation.

Haas BJ, Zeng Q, Pearson MD, Cuomo CA, Wortman JR.

Mycology. 2011 Oct 3;2(3):118-141.


[Computational approaches for identification and classification of transposable elements in eukaryotic genomes].

Xu HE, Zhang HH, Han MJ, Shen YH, Huang XZ, Xiang ZH, Zhang Z.

Yi Chuan. 2012 Aug;34(8):1009-19. Review. Chinese.


MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.

Holt C, Yandell M.

BMC Bioinformatics. 2011 Dec 22;12:491. doi: 10.1186/1471-2105-12-491.


TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.

Leroy P, Guilhot N, Sakai H, Bernard A, Choulet F, Theil S, Reboux S, Amano N, Flutre T, Pelegrin C, Ohyanagi H, Seidel M, Giacomoni F, Reichstadt M, Alaux M, Gicquello E, Legeai F, Cerutti L, Numa H, Tanaka T, Mayer K, Itoh T, Quesneville H, Feuillet C.

Front Plant Sci. 2012 Jan 31;3:5. doi: 10.3389/fpls.2012.00005. eCollection 2012.


The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes.

Estill JC, Bennetzen JL.

Plant Methods. 2009 Jun 19;5:8. doi: 10.1186/1746-4811-5-8.


Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.

Cantu D, Govindarajulu M, Kozik A, Wang M, Chen X, Kojima KK, Jurka J, Michelmore RW, Dubcovsky J.

PLoS One. 2011;6(8):e24230. doi: 10.1371/journal.pone.0024230. Epub 2011 Aug 31.


A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.

Proux-Wéra E, Armisén D, Byrne KP, Wolfe KH.

BMC Bioinformatics. 2012 Sep 17;13:237. doi: 10.1186/1471-2105-13-237.


AGeS: a software system for microbial genome sequence annotation.

Kumar K, Desai V, Cheng L, Khitrov M, Grover D, Satya RV, Yu C, Zavaljevski N, Reifman J.

PLoS One. 2011 Mar 7;6(3):e17469. doi: 10.1371/journal.pone.0017469.


Using comparative genome analysis to identify problems in annotated microbial genomes.

Poptsova MS, Gogarten JP.

Microbiology. 2010 Jul;156(Pt 7):1909-17. doi: 10.1099/mic.0.033811-0. Epub 2010 Apr 29. Review.


Saccharomyces cerevisiae: gene annotation and genome variability, state of the art through comparative genomics.

Louis E.

Methods Mol Biol. 2011;759:31-40. doi: 10.1007/978-1-61779-173-4_2.


VIGOR, an annotation program for small viral genomes.

Wang S, Sundaram JP, Spiro D.

BMC Bioinformatics. 2010 Sep 7;11:451. doi: 10.1186/1471-2105-11-451.


FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum.

Wong P, Walter M, Lee W, Mannhaupt G, Münsterkötter M, Mewes HW, Adam G, Güldener U.

Nucleic Acids Res. 2011 Jan;39(Database issue):D637-9. doi: 10.1093/nar/gkq1016. Epub 2010 Nov 4.


RAPYD--rapid annotation platform for yeast data.

Schneider J, Blom J, Jaenicke S, Linke B, Brinkrolf K, Neuweger H, Tauch A, Goesmann A.

J Biotechnol. 2011 Aug 20;155(1):118-26. doi: 10.1016/j.jbiotec.2010.10.076. Epub 2010 Oct 30.


EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome.

Thibaud-Nissen F, Campbell M, Hamilton JP, Zhu W, Buell CR.

BMC Genomics. 2007 Oct 25;8:388.


A beginner's guide to eukaryotic genome annotation.

Yandell M, Ence D.

Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. Review.


From data to function: functional modeling of poultry genomics data.

McCarthy FM, Lyons E.

Poult Sci. 2013 Sep;92(9):2519-29. doi: 10.3382/ps.2012-02808.


Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote.

Liu S, Zhang Y, Zhou Z, Waldbieser G, Sun F, Lu J, Zhang J, Jiang Y, Zhang H, Wang X, Rajendran KV, Khoo L, Kucuktas H, Peatman E, Liu Z.

BMC Genomics. 2012 Nov 5;13:595. doi: 10.1186/1471-2164-13-595.


Automatic annotation of eukaryotic genes, pseudogenes and promoters.

Solovyev V, Kosarev P, Seledsov I, Vorobyev D.

Genome Biol. 2006;7 Suppl 1:S10.1-12. Epub 2006 Aug 7.


RNA-Seq improves annotation of protein-coding genes in the cucumber genome.

Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K.

BMC Genomics. 2011 Nov 2;12:540. doi: 10.1186/1471-2164-12-540.

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