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Items: 1 to 20 of 117

1.

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.

2.

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.

Ribeiro A, Golicz A, Hackett CA, Milne I, Stephen G, Marshall D, Flavell AJ, Bayer M.

BMC Bioinformatics. 2015 Nov 11;16:382. doi: 10.1186/s12859-015-0801-z.

3.
4.

SNPMeta: SNP annotation and SNP metadata collection without a reference genome.

Kono TJ, Seth K, Poland JA, Morrell PL.

Mol Ecol Resour. 2014 Mar;14(2):419-25. doi: 10.1111/1755-0998.12183. Epub 2013 Nov 16.

PMID:
24237904
5.

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP.

Grant JR, Arantes AS, Liao X, Stothard P.

Bioinformatics. 2011 Aug 15;27(16):2300-1. doi: 10.1093/bioinformatics/btr372. Epub 2011 Jun 22.

6.

Snat: a SNP annotation tool for bovine by integrating various sources of genomic information.

Jiang J, Jiang L, Zhou B, Fu W, Liu JF, Zhang Q.

BMC Genet. 2011 Oct 7;12:85. doi: 10.1186/1471-2156-12-85.

7.

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence.

You FM, Huo N, Deal KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OD.

BMC Genomics. 2011 Jan 25;12:59. doi: 10.1186/1471-2164-12-59.

8.

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.

9.

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.

10.

Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing.

Djari A, Esquerré D, Weiss B, Martins F, Meersseman C, Boussaha M, Klopp C, Rocha D.

BMC Genomics. 2013 May 7;14:307. doi: 10.1186/1471-2164-14-307.

11.

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.

Panitz F, Stengaard H, Hornshøj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Høj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jørgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C.

Bioinformatics. 2007 Jul 1;23(13):i387-91.

PMID:
17646321
12.

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.

Milano I, Babbucci M, Panitz F, Ogden R, Nielsen RO, Taylor MI, Helyar SJ, Carvalho GR, Espiñeira M, Atanassova M, Tinti F, Maes GE, Patarnello T; FishPopTrace Consortium, Bargelloni L.

PLoS One. 2011;6(11):e28008. doi: 10.1371/journal.pone.0028008. Epub 2011 Nov 22.

13.

Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): a model for conservation genomics.

Seabury CM, Bhattarai EK, Taylor JF, Viswanathan GG, Cooper SM, Davis DS, Dowd SE, Lockwood ML, Seabury PM.

PLoS One. 2011 Jan 19;6(1):e15811. doi: 10.1371/journal.pone.0015811. Erratum in: PLoS One. 2011;6(2). doi: 10.1371/annotation/80c6965b-ffa0-4100-8a20-3f41a08b2894.

14.

Deep sequencing of Danish Holstein dairy cattle for variant detection and insight into potential loss-of-function variants in protein coding genes.

Das A, Panitz F, Gregersen VR, Bendixen C, Holm LE.

BMC Genomics. 2015 Dec 9;16:1043. doi: 10.1186/s12864-015-2249-y.

15.

SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.

Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.

BMC Bioinformatics. 2011 May 5;12:134. doi: 10.1186/1471-2105-12-134.

16.

Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery.

Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS.

BMC Genomics. 2011 Nov 15;12:559. doi: 10.1186/1471-2164-12-559.

17.

SNP discovery in nonmodel organisms: strand bias and base-substitution errors reduce conversion rates.

Gonçalves da Silva A, Barendse W, Kijas JW, Barris WC, McWilliam S, Bunch RJ, McCullough R, Harrison B, Hoelzel AR, England PR.

Mol Ecol Resour. 2015 Jul;15(4):723-36. doi: 10.1111/1755-0998.12343. Epub 2014 Nov 23.

PMID:
25388640
18.

Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes.

Reumerman RA, Tucker NP, Herron PR, Hoskisson PA, Sangal V.

Antonie Van Leeuwenhoek. 2013 Sep;104(3):431-4. doi: 10.1007/s10482-013-9953-x. Epub 2013 Jul 5.

PMID:
23828175
19.

Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design.

Field HI, Scollen SA, Luccarini C, Baynes C, Morrison J, Dunning AM, Easton DF, Pharoah PD.

BMC Bioinformatics. 2009 Jun 12;10:180. doi: 10.1186/1471-2105-10-180.

20.

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.

Haznedaroglu BZ, Reeves D, Rismani-Yazdi H, Peccia J.

BMC Bioinformatics. 2012 Jul 18;13:170. doi: 10.1186/1471-2105-13-170.

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