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GenomeGems: evaluation of genetic variability from deep sequencing data.

Ben-Zvi S, Givati A, Shomron N.

BMC Res Notes. 2012 Jul 2;5:338. doi: 10.1186/1756-0500-5-338.


Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.

Ting JC, Ye Y, Thomas GH, Ruczinski I, Pevsner J.

BMC Bioinformatics. 2006 Jan 18;7:25.


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.


An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

Yang JO, Hwang S, Oh J, Bhak J, Sohn TK.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S19. doi: 10.1186/1471-2105-9-S12-S19.


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.


High-throughput identification, database storage and analysis of SNPs in EST sequences.

Useche FJ, Gao G, Harafey M, Rafalski A.

Genome Inform. 2001;12:194-203.


snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

Leekitcharoenphon P, Kaas RS, Thomsen MC, Friis C, Rasmussen S, Aarestrup FM.

BMC Genomics. 2012;13 Suppl 7:S6. doi: 10.1186/1471-2164-13-S7-S6. Epub 2012 Dec 13.


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.


LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

Ryan M, Diekhans M, Lien S, Liu Y, Karchin R.

Bioinformatics. 2009 Jun 1;25(11):1431-2. doi: 10.1093/bioinformatics/btp242. Epub 2009 Apr 15.


WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations.

Wangkumhang P, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, Assawamakin A, Tongsima S.

BMC Genomics. 2007 Aug 14;8:275.


VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.

Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W54-8. doi: 10.1093/nar/gks572. Epub 2012 Jun 11.


QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species.

Tang J, Vosman B, Voorrips RE, van der Linden CG, Leunissen JA.

BMC Bioinformatics. 2006 Oct 9;7:438.


SNP-VISTA: an interactive SNP visualization tool.

Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, Dubchak IL.

BMC Bioinformatics. 2005 Dec 8;6:292.


Visualization of genomic aberrations using Affymetrix SNP arrays.

Müller A, Holzmann K, Kestler HA.

Bioinformatics. 2007 Feb 15;23(4):496-7. Epub 2006 Nov 30.


Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays.

Laakso M, Tuupanen S, Karhu A, Lehtonen R, Aaltonen LA, Hautaniemi S.

Bioinformatics. 2007 Aug 1;23(15):1952-61. Epub 2007 May 17.


MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation.

Hou H, Zhao F, Zhou L, Zhu E, Teng H, Li X, Bao Q, Wu J, Sun Z.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W732-6. doi: 10.1093/nar/gkq302. Epub 2010 May 5.


PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila.

Pandey RV, Kofler R, Orozco-terWengel P, Nolte V, Schlötterer C.

BMC Genet. 2011 Mar 2;12:27. doi: 10.1186/1471-2156-12-27.


CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.

Gai X, Perin JC, Murphy K, O'Hara R, D'arcy M, Wenocur A, Xie HM, Rappaport EF, Shaikh TH, White PS.

BMC Bioinformatics. 2010 Feb 4;11:74. doi: 10.1186/1471-2105-11-74.


SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock.

Nicolazzi EL, Picciolini M, Strozzi F, Schnabel RD, Lawley C, Pirani A, Brew F, Stella A.

BMC Genomics. 2014 Feb 11;15:123. doi: 10.1186/1471-2164-15-123.

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