Kaviar: An accessible system for testing SNV novelty

Bioinformatics

Volumn 27, Issue 22, 2011, Pages 3216-3217

  Glusman, Gustavo ^a   Caballero, Juan ^a   Mauldin, Denise E ^a   Hood, Leroy ^a   Roach, Jared C ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; COMPUTER PROGRAM; GENETIC VARIABILITY; GENOMICS; HUMAN; NUCLEIC ACID DATABASE;

DATABASES, NUCLEIC ACID; GENETIC VARIATION; GENOMICS; HUMANS; SOFTWARE; TRANSCRIPTOME;

EID: 80755144056     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr540     Document Type: Note

References (22)

1. 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
2. Amigo,J. et al. (2011) ENGINES: exploring single nucleotide variation in entire human genomes. BMC Bioinformatics, 12, 105.
3. Auffray,C. et al. (2009) Systems medicine: the future of medical genomics and healthcare. Genome Med., 1, 2.
4. Blekhman,R. et al. (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Res., 20, 180-189.
5. Danecek,P. et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156-2158.
6. Day,I.N.M. (2010) dbSNP in the detail and copy number complexities. Hum. Mutat., 31, 2-4.
7. Green,R.E. et al. (2010) A draft sequence of the Neanderthal genome. Science, 328, 710-722.
8. Kent,W.J. (2002). BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
9. Koboldt,D.C. et al. (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics, 25, 2283-2285.
10. Hubley,R.M. et al. (2003) Evolutionary algorithms for the selection of single nucleotide polymorphisms. BMC Bioinformatics, 4, 30.
11. Li,Y. et al. (2010) Resequencing of 200 human exomes identifies an excess of lowfrequency non-synonymous coding variants. Nat. Genet., 42, 969-972.
12. Ngamphiw,C. et al. (2011) PanSNPdb: the Pan-Asian SNP genotyping database. PLoS One, 6, e21451.
13. Paananen,J. et al. (2010) Varietas: a functional variation database portal. Database, 2010, baq016.
14. Pelak,K. et al. (2010) The characterization of twenty sequenced human genomes. PLoS Genet., 6, e1001111.
15. Rasmussen,M. et al. (2010) Ancient human genome sequence of an extinct palaeoeskimo. Nature, 463, 757-762.
16. Reese,M.G. et al. (2010)Astandard variation file format for human genome sequences. Genome Biol., 11, R88.
17. Roach,J.C. et al. (2006) Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden. Am. J. Hum. Genet., 79, 614-627.
18. Roach,J.C. et al. (2010) Analysis of genetic inheritance in a family quartet by wholegenome sequencing. Science, 328, 636-639.
19. Schuster,S.C. et al. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature, 463, 943-947.
20. Sherry,S.T. et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
21. Shetty,A.C. et al. (2010) SeqAnt: a web service to rapidly identify and annotate DNA sequence variations. BMC Bioinformatics, 11, 471.
22. Wang,E.T. et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.