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Items: 1 to 20 of 291

1.

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.

PMID:
22192575
2.

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.

Seaver SM, Gerdes S, Frelin O, Lerma-Ortiz C, Bradbury LM, Zallot R, Hasnain G, Niehaus TD, El Yacoubi B, Pasternak S, Olson R, Pusch G, Overbeek R, Stevens R, de Crécy-Lagard V, Ware D, Hanson AD, Henry CS.

Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9645-50. doi: 10.1073/pnas.1401329111.

PMID:
24927599
3.

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.

Testa AC, Hane JK, Ellwood SR, Oliver RP.

BMC Genomics. 2015 Mar 11;16:170. doi: 10.1186/s12864-015-1344-4.

PMID:
25887563
4.

GASS: genome structural annotation for Eukaryotes based on species similarity.

Wang Y, Chen L, Song N, Lei X.

BMC Genomics. 2015 Mar 4;16:150. doi: 10.1186/s12864-015-1353-3.

PMID:
25764973
5.

Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms.

Doran AG, Creevey CJ.

BMC Bioinformatics. 2013 Feb 8;14:45. doi: 10.1186/1471-2105-14-45.

PMID:
23390980
6.

PANNOTATOR: an automated tool for annotation of pan-genomes.

Santos AR, Barbosa E, Fiaux K, Zurita-Turk M, Chaitankar V, Kamapantula B, Abdelzaher A, Ghosh P, Tiwari S, Barve N, Jain N, Barh D, Silva A, Miyoshi A, Azevedo V.

Genet Mol Res. 2013 Aug 16;12(3):2982-9. doi: 10.4238/2013.August.16.2.

PMID:
24065654
7.

CycADS: an annotation database system to ease the development and update of BioCyc databases.

Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S.

Database (Oxford). 2011 Apr 7;2011:bar008. doi: 10.1093/database/bar008.

PMID:
21474551
8.

RATT: Rapid Annotation Transfer Tool.

Otto TD, Dillon GP, Degrave WS, Berriman M.

Nucleic Acids Res. 2011 May;39(9):e57. doi: 10.1093/nar/gkq1268.

PMID:
21306991
9.

Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.

Lopez D, Casero D, Cokus SJ, Merchant SS, Pellegrini M.

BMC Bioinformatics. 2011 Jul 12;12:282. doi: 10.1186/1471-2105-12-282.

PMID:
21749710
10.

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.

PMID:
21408217
11.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.

BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.

PMID:
22480257
12.

MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.

Lugli GA, Milani C, Mancabelli L, van Sinderen D, Ventura M.

FEMS Microbiol Lett. 2016 Apr;363(7). pii: fnw049. doi: 10.1093/femsle/fnw049.

PMID:
26936607
13.

Comparison of RefSeq protein-coding regions in human and vertebrate genomes.

Fong JH, Murphy TD, Pruitt KD.

BMC Genomics. 2013 Sep 25;14:654. doi: 10.1186/1471-2164-14-654.

PMID:
24063302
14.

Gene prediction and annotation in Penstemon (Plantaginaceae): A workflow for marker development from extremely low-coverage genome sequencing.

Blischak PD, Wenzel AJ, Wolfe AD.

Appl Plant Sci. 2014 Dec 4;2(12). pii: apps.1400044. doi: 10.3732/apps.1400044.

PMID:
25506519
15.

FastAnnotator--an efficient transcript annotation web tool.

Chen TW, Gan RC, Wu TH, Huang PJ, Lee CY, Chen YY, Chen CC, Tang P.

BMC Genomics. 2012;13 Suppl 7:S9. doi: 10.1186/1471-2164-13-S7-S9.

PMID:
23281853
16.

CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting.

Münz M, Ruark E, Renwick A, Ramsay E, Clarke M, Mahamdallie S, Cloke V, Seal S, Strydom A, Lunter G, Rahman N.

Genome Med. 2015 Jul 28;7:76. doi: 10.1186/s13073-015-0195-6.

PMID:
26315209
17.

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data.

Barozzi I, Termanini A, Minucci S, Natoli G.

Biol Direct. 2011 Oct 6;6:51. doi: 10.1186/1745-6150-6-51.

PMID:
21978789
18.

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.

Vijay N, Poelstra JW, Künstner A, Wolf JB.

Mol Ecol. 2013 Feb;22(3):620-34. doi: 10.1111/mec.12014.

PMID:
22998089
19.

FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression.

Paschall JE, Oleksiak MF, VanWye JD, Roach JL, Whitehead JA, Wyckoff GJ, Kolell KJ, Crawford DL.

BMC Genomics. 2004 Dec 20;5(1):96.

PMID:
15610557
20.

GPAT: retrieval of genomic annotation from large genomic position datasets.

Krebs A, Frontini M, Tora L.

BMC Bioinformatics. 2008 Dec 15;9:533. doi: 10.1186/1471-2105-9-533.

PMID:
19077303
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