Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
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.
Allows users to develop multiplex primer schemes. Primal Scheme is a web application which is able to design amplicon-based sequencing of RNA virus genomes directly from clinical samples. This platform first produces a set of candidate primer that are then ranked and scored to lastly reports to the user the primer sequences that obtains the lesser score. It includes options allowing the user to set the desired amplicon length as well as needed overlap.
Predicts primer location and polymerase chain reaction (PCR) product sequences from chromosome lists, whole genomes or circular DNA. FastPCR is an integrated tool that finds all possible primer pairs for conventional or multiplex PCR taking into account mismatches located within the specified primer or target sequence. It performs advanced searching for two or more sequences linked to each other and located within a certain distance.
Evaluates the fitness of primers. PDA is a web interface primer design service combined with thermodynamic theory. It produces optimal and homogenous primer pairs that meet the need in experimental design with large scaled polymerase chain reaction (PCR) amplifications. It allows multiple sequence query in a batch-wise mode. This application is case-insensitive, and characters other than the typical ‘ATCG’ are replaced by ‘N’.
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.
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.
Designs all possible feasible and valid primer pairs for an entire DNA database. MRPrimer takes a DNA sequence database and a set of filtering constraints as input, and then, over seven steps, it returns all feasible and valid primer pairs that exist in the database.
This tool was developed to meet the demands of primer design for highly variable sets of aligned sequences. It includes design requirements for next-generation sequences (NGS) including 454 sequences. It can also be used for primer and probe design for PCR, Sanger sequencing, and other systems with custom barcodes and DNA handles for universal primer annealing. The tool will design several alternative primer sets, whenever possible.
Calculates covariance scores for constrained regions of background conservation. McBASC can be utilized as a covarying or highly conserved filter. This software gives an equally high score to conserved or covarying alignments and allows, without a reduction in score, substitution of conserved pairs of residues for covarying ones.
Detects microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander locates microsatellite arrays within user-selected repeat classes by making correspond regular expression pattern within each DNA sequence. It employs alphabetical, noncomplementary designation, as well as repeat sequences to discover repeat sequences. This tool considers only primer pairs when they are at least 10-bp distant from the start and stop positions of the detected array.
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.
Designs minimally degenerate primers for comparative studies of multiple species. Primaclade is a web-based primer prediction application that provides a solution for researchers who want to design Polymerase Chain Reaction (PCR) primers across multiple species. The software generally performed best with alignments of up to about eight sequences and up to 29.0% sequence divergence. It can simplify the design of PCR primers for any comparative molecular study.
Automates gene-based polymerase chain reaction (PCR) primer design process. AcePrimer was developed to search for deletion alleles in Caenorhabditis elegans gene knockout experiments. It uses electronic PCR to search the entire genomic DNA sequence for potential false priming or multiple PCR amplification targets. This application provides features as the ability to target specific exons with the ‘poison primer’ approach or the evaluation of primers with electronic PCR.
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.
Generates and filters recombinase polymerase amplification (RPA) primers and exo probe sets specific for target DNA sequences in an automatic way. PrimedRPA is permissive to the presence of single nucleotide polymorphisms (SNPs) and can align several target sequences to take into account the high genetic diversity of circulating pathogens. Users can choose to score individual primers and probe in each set according to their ability to bind to potential background DNA.
Designs polymerase chain reaction (PCR) primers from DNA sequence. primer3_masker identifies and masks problematic and failure-prone regions in PCR with a repeat detection process built on a statistical model. This repeat detection function is based on k-mer frequency and can be applied to any sequences genome. This tool is available as a command line software and as a web-based application.
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.
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.
Represents a genome-aware primer pair design algorithm. ThermoAlign is able to use prior information on the locations of genomic variants during the selection of primer pairs. In order to design primer pairs forming amplicon tiling paths, a directed graph analysis method is used by this tool. It simplifies targeted genome sequence studies for any species.
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.
Generates automatically well-calibrated discrimination conditions for allele specific polymerase chain reaction (AS-PCR) assay. WASP is a web application that assists scientists in getting single nucleotide polymorphism (SNP) information from local SNP database, mirrored from all major public databases, to design AS primers for existing SNPs. The software can design AS primers for human SNPs as well as mutations.
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.
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.
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.
Allows users to predict mouse genes. Blast Primer allows identification of real-time polymerase chain reaction (PCR) primer candidates for cDNAs of interest for the deer mouse that can be used for quantitative expression analysis. It can examine expression of a variety of T cell differentiation and antiviral genes in lymph node cell recall assays from deer mice infected with the Andes virus (ANDV).
Designs sequence specific primers for a given uploaded set of target sequences. Primique identifies family member in sample of gene families and allows to upload the sequences from the gene family. This software permits the application of strict criteria and the possibility to save the found primers. As a result, each primer pair is produced to enhance its target sequence and no others in the set.
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.
Allows detection of multiple primers or oligonucleotides for genic regions. MPrime is a web application that assists molecular biologists in constructing a large number of primers and/or oligonucleotides for genes that need to have consistent properties. It also permits users to report or to test multiple sub-optimal results. It provides primer products with primer pairs and oligonucleotides that produce uniquely identifying regions.
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.
Provides a central resource for researchers conducting all types of overlapping PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online. STITCHER can handle both single sequence and multi-sequence input, and specific features facilitate numerous other PCR applications, including assembly PCR, adapter PCR, and primer walking.
Scans automatically target DNA sequences and designs primers in regions of low degeneracy that are free of secondary structures (hairpins, dimers and false priming sites). Primer Premier searches for optimal polymerase chain reaction (PCR), multiplex and single nucleotide polymorphism (SNP) genotyping primers via a nearest neighbor algorithm. It supports multiplex assays and can automatically describe BLAST search results.
Provides a solution for proteomic compression. FlexGrePPS is an algorithm for the construction of near optimal sets of degenerate peptide pools that lend themselves to rapid and economical screening of the entire proteome of an organism. This method is also applicable to nucleotide sequences and outperforms most DNA primer selection programs. Although, FlexGrePPS was designed for computing performance to handle very large data sets.
A web-based primer design tool for the specific amplification of individual members of multigenic families across related species and also to evaluate the differential expression of isogenes for a given species.
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.
Designs high-throughput specific primers. The workflow of PrimerServer consists of three steps: (i) primer design, primer specificity check, and data integration, (ii) sequences of candidate primer pairs are extracted and used as queries in BLAST searches, and (iii) it sorts the potential primer pairs by the number of possible PCR amplicons and then by the penalty score from Primer3, and displays them in a pretty-formatted web page.
Addresses the challenges of bacterial identification, pathogen detection or species identification. AlleleID is a comprehensive desktop tool to design species identification/cross species probes for microarrays or real time polymerase chain reaction (PCR) including SYBR Green, TaqMan MGB, TaqMan probes, Molecular Beacons and real time PCR primers. AlleleID also offers support for designing microarray experiments for detecting alternative splicing events.
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.