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Items: 1 to 20 of 180

1.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.

Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M.

Bioinformatics. 2012 Sep 1;28(17):2267-9. Epub 2012 Jun 28.

2.

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.

3.

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing.

Zhao S, Prenger K, Smith L, Messina T, Fan H, Jaeger E, Stephens S.

BMC Genomics. 2013 Jun 27;14:425. doi: 10.1186/1471-2164-14-425.

4.

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR.

Yang H, Wang K.

Nat Protoc. 2015 Oct;10(10):1556-66. doi: 10.1038/nprot.2015.105. Epub 2015 Sep 17.

PMID:
26379229
5.

MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions.

Garla V, Kong Y, Szpakowski S, Krauthammer M.

Bioinformatics. 2011 Feb 1;27(3):416-8. doi: 10.1093/bioinformatics/btq658. Epub 2010 Dec 12.

6.

wANNOVAR: annotating genetic variants for personal genomes via the web.

Chang X, Wang K.

J Med Genet. 2012 Jul;49(7):433-6. doi: 10.1136/jmedgenet-2012-100918. Epub 2012 Jun 20.

7.

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group.

Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.

8.

Atlas2 Cloud: a framework for personal genome analysis in the cloud.

Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F.

BMC Genomics. 2012;13 Suppl 6:S19. doi: 10.1186/1471-2164-13-S6-S19. Epub 2012 Oct 26.

9.

SeqAnt: a web service to rapidly identify and annotate DNA sequence variations.

Shetty AC, Athri P, Mondal K, Horner VL, Steinberg KM, Patel V, Caspary T, Cutler DJ, Zwick ME.

BMC Bioinformatics. 2010 Sep 20;11:471. doi: 10.1186/1471-2105-11-471.

10.

The personal genome browser: visualizing functions of genetic variants.

Juan L, Teng M, Zang T, Hao Y, Wang Z, Yan C, Liu Y, Li J, Zhang T, Wang Y.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W192-7. doi: 10.1093/nar/gku361. Epub 2014 May 5.

11.

Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.

San Lucas FA, Wang G, Scheet P, Peng B.

Bioinformatics. 2012 Feb 1;28(3):421-2. doi: 10.1093/bioinformatics/btr667. Epub 2011 Dec 2.

12.

Prokka: rapid prokaryotic genome annotation.

Seemann T.

Bioinformatics. 2014 Jul 15;30(14):2068-9. doi: 10.1093/bioinformatics/btu153. Epub 2014 Mar 18.

13.

Variant association tools for quality control and analysis of large-scale sequence and genotyping array data.

Wang GT, Peng B, Leal SM.

Am J Hum Genet. 2014 May 1;94(5):770-83. doi: 10.1016/j.ajhg.2014.04.004.

14.

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.

Wang K, Li M, Hakonarson H.

Nucleic Acids Res. 2010 Sep;38(16):e164. doi: 10.1093/nar/gkq603. Epub 2010 Jul 3.

15.

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.

16.

A geometric approach for classification and comparison of structural variants.

Sindi S, Helman E, Bashir A, Raphael BJ.

Bioinformatics. 2009 Jun 15;25(12):i222-30. doi: 10.1093/bioinformatics/btp208.

17.

SG-ADVISER CNV: copy-number variant annotation and interpretation.

Erikson GA, Deshpande N, Kesavan BG, Torkamani A.

Genet Med. 2015 Sep;17(9):714-8. doi: 10.1038/gim.2014.180. Epub 2014 Dec 18.

18.

Annotation of functional variation in personal genomes using RegulomeDB.

Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M.

Genome Res. 2012 Sep;22(9):1790-7. doi: 10.1101/gr.137323.112.

19.

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.

20.

VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants.

Ho ED, Cao Q, Lee SD, Yip KY.

BMC Genomics. 2014 Oct 11;15:886. doi: 10.1186/1471-2164-15-886.

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