Literature DB >> 15215373

SNPbox: web-based high-throughput primer design from gene to genome.

Stefan Weckx1, Peter De Rijk, Christine Van Broeckhoven, Jurgen Del-Favero.   

Abstract

SNPbox is a modular software package that automates the design of PCR primers for large-scale amplification and sequencing projects in a standardized manner resulting in high-quality PCR amplicons with a low failure rate. Here, we present the SNPbox web server at http://www.SNPbox.org, which hosts the SNPbox web service as well as the data from SNPbox analysis of all Ensembl exons. The data of this genome-wide SNPbox application can be visualized in Ensembl's ContigView through a DAS (distributed annotation system) annotation server.

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Year:  2004        PMID： 15215373      PMCID： PMC441507          DOI： 10.1093/nar/gkh369

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  13 in total

1.  Primer3 on the WWW for general users and for biologist programmers.

Authors:  S Rozen; H Skaletsky
Journal:  Methods Mol Biol       Date:  2000

2.  The Ensembl genome database project.

Authors:  T Hubbard; D Barker; E Birney; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; L Huminiecki; A Kasprzyk; H Lehvaslaiho; P Lijnzaad; C Melsopp; E Mongin; R Pettett; M Pocock; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; M Clamp
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  Spidey: a tool for mRNA-to-genomic alignments.

Authors:  S J Wheelan; D M Church; J M Ostell
Journal:  Genome Res       Date:  2001-11       Impact factor: 9.043

4.  Ensembl 2004.

Authors:  E Birney; D Andrews; P Bevan; M Caccamo; G Cameron; Y Chen; L Clarke; G Coates; T Cox; J Cuff; V Curwen; T Cutts; T Down; R Durbin; E Eyras; X M Fernandez-Suarez; P Gane; B Gibbins; J Gilbert; M Hammond; H Hotz; V Iyer; A Kahari; K Jekosch; A Kasprzyk; D Keefe; S Keenan; H Lehvaslaiho; G McVicker; C Melsopp; P Meidl; E Mongin; R Pettett; S Potter; G Proctor; M Rae; S Searle; G Slater; D Smedley; J Smith; W Spooner; A Stabenau; J Stalker; R Storey; A Ureta-Vidal; C Woodwark; M Clamp; T Hubbard
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  Primer Design Assistant (PDA): A web-based primer design tool.

Authors:  S H Chen; C Y Lin; C S Cho; C Z Lo; C A Hsiung
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

6.  Genome-scale design of PCR primers and long oligomers for DNA microarrays.

Authors:  Stefan A Haas; Marc Hild; Anthony P H Wright; Torsten Hain; Driss Talibi; Martin Vingron
Journal:  Nucleic Acids Res       Date:  2003-10-01       Impact factor: 16.971

7.  Primer Master: a new program for the design and analysis of PCR primers.

Authors:  V Proutski; E C Holmes
Journal:  Comput Appl Biosci       Date:  1996-06

8.  PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing.

Authors:  P Li; K C Kupfer; C J Davies; D Burbee; G A Evans; H R Garner
Journal:  Genomics       Date:  1997-03-15       Impact factor: 5.736

Review 9.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

10.  HGVbase: a curated resource describing human DNA variation and phenotype relationships.

Authors:  D Fredman; G Munns; D Rios; F Sjöholm; M Siegfried; B Lenhard; H Lehväslaiho; A J Brookes
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971
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  9 in total

1.  novoSNP, a novel computational tool for sequence variation discovery.

Authors:  Stefan Weckx; Jurgen Del-Favero; Rosa Rademakers; Lieve Claes; Marc Cruts; Peter De Jonghe; Christine Van Broeckhoven; Peter De Rijk
Journal:  Genome Res       Date:  2005-03       Impact factor: 9.043

2.  Coagulase-negative Staphylococci favor conversion of arginine into ornithine despite a widespread genetic potential for nitric oxide synthase activity.

Authors:  María Sánchez Mainar; Stefan Weckx; Frédéric Leroy
Journal:  Appl Environ Microbiol       Date:  2014-10-03       Impact factor: 4.792

3.  Expression of the arginine deiminase pathway genes in Lactobacillus sakei is strain dependent and is affected by the environmental pH.

Authors:  T Rimaux; A Rivière; K Illeghems; S Weckx; L De Vuyst; F Leroy
Journal:  Appl Environ Microbiol       Date:  2012-04-27       Impact factor: 4.792

4.  The ability of bifidobacteria to degrade arabinoxylan oligosaccharide constituents and derived oligosaccharides is strain dependent.

Authors:  Audrey Rivière; Frédéric Moens; Marija Selak; Dominique Maes; Stefan Weckx; Luc De Vuyst
Journal:  Appl Environ Microbiol       Date:  2013-10-18       Impact factor: 4.792

5.  SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.

Authors:  Lin Wang; Simin Liu; Tianhua Niu; Xin Xu
Journal:  BMC Bioinformatics       Date:  2005-03-18       Impact factor: 3.169

6.  RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

Authors:  Jittima Piriyapongsa; Chumpol Ngamphiw; Anunchai Assawamakin; Pongsakorn Wangkumhang; Payiarat Suwannasri; Uttapong Ruangrit; Gallissara Agavatpanitch; Sissades Tongsima
Journal:  BMC Genomics       Date:  2009-12-03       Impact factor: 3.969

7.  Genes for hereditary sensory and autonomic neuropathies: a genotype-phenotype correlation.

Authors:  Annelies Rotthier; Jonathan Baets; Els De Vriendt; An Jacobs; Michaela Auer-Grumbach; Nicolas Lévy; Nathalie Bonello-Palot; Sara Sebnem Kilic; Joachim Weis; Andrés Nascimento; Marielle Swinkels; Moyo C Kruyt; Albena Jordanova; Peter De Jonghe; Vincent Timmerman
Journal:  Brain       Date:  2009-08-03       Impact factor: 13.501

8.  Mutations in the SPTLC2 subunit of serine palmitoyltransferase cause hereditary sensory and autonomic neuropathy type I.

Authors:  Annelies Rotthier; Michaela Auer-Grumbach; Katrien Janssens; Jonathan Baets; Anke Penno; Leonardo Almeida-Souza; Kim Van Hoof; An Jacobs; Els De Vriendt; Beate Schlotter-Weigel; Wolfgang Löscher; Petr Vondráček; Pavel Seeman; Peter De Jonghe; Patrick Van Dijck; Albena Jordanova; Thorsten Hornemann; Vincent Timmerman
Journal:  Am J Hum Genet       Date:  2010-10-08       Impact factor: 11.025

9.  Novel variants of major drug-metabolising enzyme genes in diverse African populations and their predicted functional effects.

Authors:  Alice Matimba; Jurgen Del-Favero; Christine Van Broeckhoven; Collen Masimirembwa
Journal:  Hum Genomics       Date:  2009-01       Impact factor: 4.639
  9 in total

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