Dataset Information

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.

ABSTRACT:

Motivation

PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task.

Results

PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.

Availability

PrimerProspector is open-source software available at http://pprospector.sourceforge.net

Contact

rob.knight@colorado.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Walters WA

PROVIDER: S-EPMC3072552 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.

Walters William A WA Caporaso J Gregory JG Lauber Christian L CL Berg-Lyons Donna D Fierer Noah N Knight Rob R

Bioinformatics (Oxford, England) 20110223 8

<h4>Motivation</h4>PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task.<h4>Results</h4>PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.<h4>Availability</h4>PrimerProspector ...[more]

PMID: 21349862

Similar Datasets

Project description:BackgroundChoosing appropriate primers is probably the single most important factor affecting the polymerase chain reaction (PCR). Specific amplification of the intended target requires that primers do not have matches to other targets in certain orientations and within certain distances that allow undesired amplification. The process of designing specific primers typically involves two stages. First, the primers flanking regions of interest are generated either manually or using software tools; then they are searched against an appropriate nucleotide sequence database using tools such as BLAST to examine the potential targets. However, the latter is not an easy process as one needs to examine many details between primers and targets, such as the number and the positions of matched bases, the primer orientations and distance between forward and reverse primers. The complexity of such analysis usually makes this a time-consuming and very difficult task for users, especially when the primers have a large number of hits. Furthermore, although the BLAST program has been widely used for primer target detection, it is in fact not an ideal tool for this purpose as BLAST is a local alignment algorithm and does not necessarily return complete match information over the entire primer range.ResultsWe present a new software tool called Primer-BLAST to alleviate the difficulty in designing target-specific primers. This tool combines BLAST with a global alignment algorithm to ensure a full primer-target alignment and is sensitive enough to detect targets that have a significant number of mismatches to primers. Primer-BLAST allows users to design new target-specific primers in one step as well as to check the specificity of pre-existing primers. Primer-BLAST also supports placing primers based on exon/intron locations and excluding single nucleotide polymorphism (SNP) sites in primers.ConclusionsWe describe a robust and fully implemented general purpose primer design tool that designs target-specific PCR primers. Primer-BLAST offers flexible options to adjust the specificity threshold and other primer properties. This tool is publicly available at http://www.ncbi.nlm.nih.gov/tools/primer-blast.

Dataset Information

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.

Motivation

Results

Availability

Contact

Supplementary information

Publications

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.

Similar Datasets

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