Literature DB >> 14962918

Amplicon: software for designing PCR primers on aligned DNA sequences.

Simon N Jarman1.   

Abstract

SUMMARY: Amplicon is a program for designing PCR primers on aligned groups of DNA sequences. The most important application for Amplicon is the design of 'group-specific' PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. AVAILABILITY: Amplicon is freely available as a script that will run on any platform with Python 2.3 installed (http://www.python.org). It is also available as a Windows executable. Free downloads that do not require registration can be found at http://www.aad.gov.au/amplicon

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Year:  2004        PMID： 14962918     DOI： 10.1093/bioinformatics/bth121

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  19 in total

1.  PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.

Authors:  Qing Yu; Elizabeth M Ryan; Todd M Allen; Bruce W Birren; Matthew R Henn; Niall J Lennon
Journal:  Bioinformatics       Date:  2010-11-09       Impact factor: 6.937

2.  ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.

Authors:  Tiayyba Riaz; Wasim Shehzad; Alain Viari; François Pompanon; Pierre Taberlet; Eric Coissac
Journal:  Nucleic Acids Res       Date:  2011-09-19       Impact factor: 16.971

3.  A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil.

Authors:  Jason D Gans; John Dunbar; Stephanie A Eichorst; La Verne Gallegos-Graves; Murray Wolinsky; Cheryl R Kuske
Journal:  Nucleic Acids Res       Date:  2012-03-20       Impact factor: 16.971

4.  Genome-wide selection of unique and valid oligonucleotides.

Authors:  Heikki Hyyrö; Martti Juhola; Mauno Vihinen
Journal:  Nucleic Acids Res       Date:  2005-07-26       Impact factor: 16.971

5.  primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies.

Authors:  Bruno Contreras-Moreira; Bernardo Sachman-Ruiz; Iraís Figueroa-Palacios; Pablo Vinuesa
Journal:  Nucleic Acids Res       Date:  2009-05-21       Impact factor: 16.971

6.  Multiplex primer prediction software for divergent targets.

Authors:  Shea N Gardner; Amy L Hiddessen; Peter L Williams; Christine Hara; Mark C Wagner; Bill W Colston
Journal:  Nucleic Acids Res       Date:  2009-09-16       Impact factor: 16.971

7.  iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences.

Authors:  Richard Boyce; Parmit Chilana; Timothy M Rose
Journal:  Nucleic Acids Res       Date:  2009-05-14       Impact factor: 16.971

8.  De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.

Authors:  Christopher A Gulvik; T Chad Effler; Steven W Wilhelm; Alison Buchan
Journal:  PLoS One       Date:  2012-11-26       Impact factor: 3.240

9.  PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences.

Authors:  Jiqiang Yao; Hong Lin; Allen Van Deynze; Harshavardhan Doddapaneni; Martha Francis; Eliana Gertrudes Macedo Lemos; Edwin L Civerolo
Journal:  BMC Microbiol       Date:  2008-10-20       Impact factor: 3.605

10.  DNA-based diet analysis for any predator.

Authors:  Glenn Dunshea
Journal:  PLoS One       Date:  2009-04-23       Impact factor: 3.240
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