Search Results for "primer3"
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Showing 11 open source projects for "primer3"
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Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
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MPprimer
a program for reliable multiplex PCR primer design
... dimerization, and the inability to separate and purify DNA amplicons of similar electrophoretic mobility. Results: A new program named MPprimer was developed to help users design primer sets for multiplex PCR with high reliability. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. -
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Auto Primer3
Automatically design primers to genes/coordinates using primer3.
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/autoprimer3) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/autoprimer3/releases/latest). AutoPrimer3 retrieves gene information, DNA sequences and SNP information from the UCSC genome browser and uses primer3 to automatically design primers to genes or genomic coordinate targets. Primers may be designed using information from any of the UCSC hosted genomes... -
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eDNAprimer
Primer design software for environmental DNA studies
eDNAprimer is a software program that facilitates the selection of primer and probe sets for quantitative PCR (qPCR) reactions. In essence, eDNAprimer uses the core functionality of Primer3 to produce a list of potential primer sets based on efficiency, but allows the user to incorporate specificity against a list of non-target sequences in the primer selection process. Multiple target sequences may also be used as input, with primer selection directed towards regions that are consistent across... -
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CEMAsuite
Consensus/Degenerate Primer Design Application
CEMAsuite, is an interactive Java-based application with the ability to (i) construct a codon-equivalent multiple alignment (CEMA) from a protein multiple sequence alignment (MSA) file, (ii) generate and score each position in the consensus DNA sequence using multiple algorithms, (iii) design single-degeneracy primer backbones using Primer3 (Untergasser et al. 2012), (iv) estimate the stability of degenerate primers on each of the coding sequences within the CEMA, and (v) export intermediate... -
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primeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to easily...
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FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra
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IMAS is a Visual Analytics system for the discovery of knowledge in genomic information. IMAS enables genomic scientists to rapidly analyze and visualize a set of microbial genomic sequences using tools such as Glimmer, Blast, Clustal-W, Primer3.
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SCAMPI is designed to rapidly detect molecular markers in silico through sequence comparison. For this purpose it creates a unique workflow integrating third party tools like NCBI Blast or Primer3.
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Autoprime
Automated primer design using EnsEMBL
AutoPrime allows to rapidly design primers for real-time PCR measurement of eukaryotic expression. By connecting to the EnsEMBL database gene structure information is used to find primers spanning exon borders. This way only expressed sequences are captured. Additionally mispriming on repetitive regions can be avoided using information from RepBase.
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