PubMed

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.PMID: 19545381 [PubMed - in process]Related articlesFree article

Combined evidence annotation of transposable elements in genome sequences.

Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D.

PLoS Comput Biol. 2005 Jul;1(2):166-75. Epub 2005 Jul 29.PMID: 16110336 [PubMed]Related articlesFree article

Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome.

Hamberger B, Hall D, Yuen M, Oddy C, Hamberger B, Keeling CI, Ritland C, Ritland K, Bohlmann J.

BMC Plant Biol. 2009 Aug 6;9:106.PMID: 19656416 [PubMed - indexed for MEDLINE]Related articlesFree article

Isolation and sequence analysis of the wheat B genome subtelomeric DNA.

Salina EA, Sergeeva EM, Adonina IG, Shcherban AB, Afonnikov DA, Belcram H, Huneau C, Chalhoub B.

BMC Genomics. 2009 Sep 5;10:414.PMID: 19732459 [PubMed - indexed for MEDLINE]Related articlesFree article

Evidence-based gene predictions in plant genomes.

Liang C, Mao L, Ware D, Stein L.

Genome Res. 2009 Oct;19(10):1912-23. Epub 2009 Jun 18.PMID: 19541913 [PubMed - indexed for MEDLINE]Related articles

IMG ER: a system for microbial genome annotation expert review and curation.

Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC.

Bioinformatics. 2009 Sep 1;25(17):2271-8. Epub 2009 Jun 27.PMID: 19561336 [PubMed - indexed for MEDLINE]Related articles

Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat.

Wanjugi H, Coleman-Derr D, Huo N, Kianian SF, Luo MC, Wu J, Anderson O, Gu YQ.

Genome. 2009 Jun;52(6):576-87.PMID: 19483776 [PubMed - indexed for MEDLINE]Related articles

Plant genome annotation methods.

Ouyang S, Thibaud-Nissen F, Childs KL, Zhu W, Buell CR.

Methods Mol Biol. 2009;513:263-82.PMID: 19347655 [PubMed - indexed for MEDLINE]Related articles

DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum.

Jing HC, Bayon C, Kanyuka K, Berry S, Wenzl P, Huttner E, Kilian A, Hammond-Kosack KE.

BMC Genomics. 2009 Sep 30;10:458.PMID: 19788762 [PubMed - indexed for MEDLINE]Related articlesFree article

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.

Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005.PMID: 16214803 [PubMed - indexed for MEDLINE]Related articlesFree article

MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.

Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M.

Genome Res. 2008 Jan;18(1):188-96. Epub 2007 Nov 19.PMID: 18025269 [PubMed - indexed for MEDLINE]Related articlesFree article

In silico microarray probe design for diagnosis of multiple pathogens.

Vijaya Satya R, Zavaljevski N, Kumar K, Bode E, Padilla S, Wasieloski L, Geyer J, Reifman J.

BMC Genomics. 2008 Oct 21;9:496.PMID: 18940003 [PubMed - indexed for MEDLINE]Related articlesFree article

Improved repeat identification and masking in Dipterans.

Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen GH.

Gene. 2007 Mar 1;389(1):1-9. Epub 2006 Oct 12.PMID: 17137733 [PubMed - indexed for MEDLINE]Related articlesFree article

DIYA: a bacterial annotation pipeline for any genomics lab.

Stewart AC, Osborne B, Read TD.

Bioinformatics. 2009 Apr 1;25(7):962-3. Epub 2009 Mar 2.PMID: 19254921 [PubMed - indexed for MEDLINE]Related articlesFree article

OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity.

Neerincx PB, Rauwerda H, Nie H, Groenen MA, Breit TM, Leunissen JA.

BMC Proc. 2009 Jul 16;3 Suppl 4:S4.PMID: 19615117 [PubMed]Related articlesFree article

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

Zdobnov EM, Campillos M, Harrington ED, Torrents D, Bork P.

Nucleic Acids Res. 2005 Feb 16;33(3):946-54. Print 2005.PMID: 15716312 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize.

Kronmiller BA, Wise RP.

Plant Physiol. 2009 Oct;151(2):483-95. Epub 2009 Aug 12.PMID: 19675151 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational annotation of genes differentially expressed along olive fruit development.

Galla G, Barcaccia G, Ramina A, Collani S, Alagna F, Baldoni L, Cultrera NG, Martinelli F, Sebastiani L, Tonutti P.

BMC Plant Biol. 2009 Oct 24;9:128.PMID: 19852839 [PubMed - indexed for MEDLINE]Related articlesFree article

The Genome Reverse Compiler: an explorative annotation tool.

Warren AS, Setubal JC.

BMC Bioinformatics. 2009 Jan 27;10:35.PMID: 19173744 [PubMed - indexed for MEDLINE]Related articlesFree article

Automated paleontology of repetitive DNA with REANNOTATE.

Pereira V.

BMC Genomics. 2008 Dec 18;9:614.PMID: 19094224 [PubMed - indexed for MEDLINE]Related articlesFree article