Literature DB >> 15073008

PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design.

Paul C Boutros1, Allan B Okey.   

Abstract

UNLABELLED: We developed a CGI/Perl-based web server to perform in silico polymerase chain reaction (PCR) on PCR primer sequences. The PUNS (Primer-UniGene Selectivity) server simulates PCR reactions by running BLASTN analysis on user-entered primer pairs against both the transcriptome and the genome to assess primer specificity. PUNS is particularly suited for the identification of highly selective primers for quantitative microarray validation. AVAILABILITY: Both system access and source-code are freely available at http://okeylabimac.med.utoronto.ca/PUNS.

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Year:  2004        PMID： 15073008     DOI： 10.1093/bioinformatics/bth257

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


  6 in total

1.  MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity.

Authors:  Wubin Qu; Yang Zhou; Yanchun Zhang; Yiming Lu; Xiaolei Wang; Dongsheng Zhao; Yi Yang; Chenggang Zhang
Journal:  Nucleic Acids Res       Date:  2012-06-11       Impact factor: 16.971

2.  Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates.

Authors:  Youfang Cao; Lianjie Wang; Kexue Xu; Chunhai Kou; Yulei Zhang; Guifang Wei; Junjian He; Yunfang Wang; Liping Zhao
Journal:  BMC Bioinformatics       Date:  2005-07-26       Impact factor: 3.169

3.  MICA: desktop software for comprehensive searching of DNA databases.

Authors:  William A Stokes; Benjamin S Glick
Journal:  BMC Bioinformatics       Date:  2006-10-03       Impact factor: 3.169

4.  KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping.

Authors:  Alsamman M Alsamman; Shafik D Ibrahim; Aladdin Hamwieh
Journal:  Bioinformatics       Date:  2019-09-01       Impact factor: 6.937

Review 5.  Designing Allele-Specific Competitive-Extension PCR-Based Assays for High-Throughput Genotyping and Gene Characterization.

Authors:  Ruslan Kalendar; Alexandr V Shustov; Ilyas Akhmetollayev; Ulykbek Kairov
Journal:  Front Mol Biosci       Date:  2022-03-01

6.  Improved assay-dependent searching of nucleic acid sequence databases.

Authors:  Jason D Gans; Murray Wolinsky
Journal:  Nucleic Acids Res       Date:  2008-05-31       Impact factor: 16.971
  6 in total

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