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MRPrimerW
A straightforward but powerful tool for designing high-quality primer pairs that can be used simultaneously to detect multiple target genes in qPCR experiments. MRPrimerW overcomes the major drawbacks of existing web servers for primer design by enabling users to freely adjust filtering constraints, performing complete homology tests, supporting batch designing for qPCR, supporting TaqMan probe design and supporting ranking of primers. These powerful features were achieved by performing large-scale computation for homology testing on all possible candidate primers in an exact manner, and then materializing the resultant valid primers in eight kinds of indices in the main memory of the web server. Based on these indices, the web server quickly performs online processing in three steps and returns a complete set of the top primer pairs corresponding to the user's query.
PCRTiler
Allows users to detect candidate primers for each sub-region. PCRTiler is composed of a webserver to automate the design of multiple specific primer pairs covering one or multiple genomic loci. It handles all aspects of the selection of candidate primer pairs using the Primer3 software and also implements the specificity check using BLAST. This tool is also available as a desktop version. It also manages all aspects of downloading genomes from GenBank and the creation of BLAST databases.
RJPrimers
Identifies repeat junctions and then designs repeat junction marker (RJM) primers. RJPrimers is a high-throughput computational tool that employs a BLASTN search and a repeat junction finding algorithm. It includes three contiguous operational steps, a BLASTN search against a repeat database, repeat junction identification and primer design. Its performance depends on the number of sequences and their sizes, the number of repeat junctions in the sequences, the size of the repeat database selected, and the speed of the computer.
msatcommander
Is designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated, FASTA-formatted files. msatcommander uses regular expression pattern matching within each DNA sequence to locate microsatellite arrays within user-selected repeat classes. Repeat sequences are located using their lowest alphabetical, noncomplementary designation, and repeat sequences fitting these designations are written to the summary output file. Search data and locus-specific primers are written to comma-separated value (CSV) files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports.
PrimerProspector
An extensible framework for primer design and analysis. PrimerProspector can be used for any nucleic acid sequences and allows users to design de novo primers based upon arbitrary multiple sequence alignments. User-specifiable design parameters include primer length, degeneracy and targeted regions for generation of primers. Existing or de novo primers can be analyzed for predicted taxonomic coverage. PrimerProspector allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.
swga
Identifies selective primer sets for a given target genome and background. swga evaluates all potential primer sequences and forms sets of valid primers. It automatically calculates a variety of metrics for each set that potentially affect the efficacy and selectivity of the reaction. These sets are then ranked and presented to the user, enabling the selection of primer sets most likely to succeed. Nearly all operating parameters of the program are user-specifiable but initialized with reasonable defaults based on the target and background genomes selected, reducing the work needed to get started.
keeSeek
A command line tool for generating, for a given reference genome, a set of k-mers absent in that genome. The main differences with respect to previously developed tools for neverwords generation are (i) calculation of the distance from the reference genome, in terms of number of mismatches, and selection of the most distant sequences that will have a low probability to anneal unspecifically; (ii) application of a series of filters to discard candidates not suitable to be used as PCR primers.
RUCS / Rapid identification of PCR primers for Unique Core Sequences
Eases the burden of Polymerase chain reaction (PCR) primer design. RUCS is a web application that allows users to (i) identify unique core sequences for a given dataset of positive and negative genomes, and (ii) combines the primer pair prediction of Primer3, with a novel in silico PCR product validation method. In this condition, RUCS can predict amplicons for PCR primer pairs against a positive and a negative set of references.
Primer-BLAST
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Helps users design target-specific primers. Primer-BLAST is a web application that offers flexibility to accommodate different primer design. It incorporates a global alignment mechanism and is designed to be very sensitive in detecting potential amplification targets. Users can either design new primers or check the specificity of pre-existing primers. Finally, it has the capability to place primers based on exon/intron boundaries and Single-Nucleotide Polymorphism (SNP) locations.
QuantPrime
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Allows primer pair design in small- to large-scale real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) analyses. QuantPrime is a web application which offers design and specificity checking with customizable parameters. The software is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops, while benefiting from exon-intron border and alternative splice variant information in available genome annotations.
Edesign
A design tool for PCR primers together with an internal probe for conducting quantitative PCR and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis.
miRprimer
Designs primers for polymerase chain reaction (PCR) amplification of microRNAs. miRprimer generates a number of putative primers based on an interpretation of the guidelines for manual primer design into computer language. The availability of automated primer design makes this method an even more attractive option for quantification of microRNA expression. Primers designed with this algorithm were tested in different experiments and have the same success rate as manually designed primers.
PhiSiGns
Provides a convenient web interface that allows biologists to perform a dynamic search against selected phage genomes of interest, identify signature genes, generate sequence alignments, and design primers for PCR amplification, all in one environment that increases efficiency and productivity. Signature genes identified using this tool can be used to build phylogenetic trees and study phage evolution. Furthermore, primers designed using PhiSiGns can be used to amplify related sequences from environmental samples to increase knowledge of uncultured phage diversity.
Primers-4-Yeast
Allows primers to be designed in batches for S. cerevisiae gene-targeting transformations, and for the validation of correct insertions. Primers-4-Yeast enables fast, automated, accurate primer planning for large sets of genes, introduces consistency in primer planning and is therefore suggested to serve as a standard in yeast research. It allows users to design primers for gene targeting of polymerase chain reaction (PCR)-based transformation cassettes into S. cerevisiae and for the validation of correct clones.
PrimerView
Designs forward and reverse primers from multi-sequence datasets, and generates graphical outputs that map the position and distribution of primers to the target sequence. This module operates from the command-line and can collect user-defined input for the design phase of each primer. PrimerView is a straightforward to use module that implements a primer design algorithm to return forward and reverse primers from any number of FASTA formatted sequences to generate text based output of the features for each primer, and also graphical outputs that map the designed primers to the target sequence.
eprimer3
Picks PCR primers and hybridization oligos. eprimer3 is an interface to the 'primer3' program from the Whitehead Institute. The Whitehead program must be set up and on the path in order for eprimer3 to find and run it. Primer3 picks primers for polymerase chain reaction (PCR), considering as criteria (i) oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities, (ii) PCR product size, (iii) positional constraints within the source sequence, and (iv) miscellaneous other constraints. eprimer3 can also pick hybridisation oligos that are internal to the product.
Beacon Designer
Automates the design of real time primers and probes. Beacon Designer is used by molecular biologists worldwide to design successful real time polymerase chain reaction (PCR) assays. It saves the time and the money involved in failed experiments. It is a flexible solution to real-time primer and probe design needs and pays for itself many times over. In addition to locating the primer anywhere on the gene of interest, Beacon Designer can design primers across exon-exon or exon-intron junctions.
CLC Main Workbench
Allows DNA, RNA, and protein sequence data analysis. CLC Main Workbench is a comprehensive workbench. A primer design functionality offers graphical interaction during the primer selection process. The software also allows to show the annotations of the individual sequences in a multiple sequence alignment, offers graphically advanced in silico cloning and design of vectors, BLAST searches on protein and DNA sequences, and other feature such as Assembly, Phylogeny, Workflow, Molecular structure visualization and development of plug-ins.
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