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.
Assists users to produce polymerase chain reaction (PCR) experiments and predict the result. Amplify is a program that requires a target sequence and primers for working. The interface of the tool allows users to obtain information about any item in the picture by clicking the mouse pointer on it.
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.