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RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
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BatchPrimer3: a high throughput web application for PCR and sequencing primer design.

Frank M You1, Naxin Huo, Yong Qiang Gu

  • 1Department of Plant Sciences, University of California, CA 95616, USA. frank.you@ars.usda.gov

BMC Bioinformatics
|May 31, 2008
PubMed
Summary

BatchPrimer3 is a new high-throughput software for designing SSR and SNP primers, streamlining genetic marker development. This tool facilitates large-scale genomic research by enabling batch primer design for various applications.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Microsatellite (SSR) and single nucleotide polymorphism (SNP) markers are crucial for genetic mapping and genotyping.
  • Large-scale genomic projects necessitate high-throughput, computer-assisted primer design.
  • Existing primer design programs often lack batch processing capabilities, creating a demand for efficient tools.

Purpose of the Study:

  • To develop a comprehensive, web-based software tool for high-throughput primer design.
  • To specifically address the need for batch primer design for SSR flanking and SNP genotyping.
  • To create a user-friendly platform based on the established Primer3 core.

Main Methods:

  • Developed BatchPrimer3, a web program utilizing the Primer3 core for primer pair selection.
  • Incorporated a novel score-based primer picking module for position-restricted primer selection.
  • Implemented batch processing for DNA sequences in FASTA format, including pre-analysis and masking options.

Main Results:

  • BatchPrimer3 supports diverse primer designs: generic, SSR with detection, SNP genotyping (SBE, allele-specific, tetra-primer ARMS), and DNA sequencing primers.
  • The program offers pre-analysis of sequences for parameter setting and allows pre-processing/masking.
  • Tab-delimited or Excel output formats facilitate primer ordering; thousands of validated primers have been designed for wheat and Brachypodium projects.

Conclusions:

  • BatchPrimer3 is a comprehensive, high-throughput web primer design program for various primer types.
  • The software architecture allows for easy integration of additional primer design methods in future versions.
  • Source code and pre-designed primers for wheat and Brachypodium are publicly available online.