Customized RNA synthesis is in demand for biological and biotechnological research. While chemical synthesis and gel or chromatographic purification of RNA is costly and difficult for sequences longer than tens of nucleotides, a pipeline of primer assembly of DNA templates, in vitro transcription by T7 RNA polymerase and kit-based purification provides a cost-effective and fast alternative for preparing RNA molecules. Nevertheless, designing template primers that optimize cost and avoid mispriming during polymerase chain reaction currently requires expert inspection, downloading specialized software or both.
Provides a web server to design for the amplification of single templates. BiSearch is a useful tool in primer design for complex matrices and especially for bisulfite-treated genomes. It can be utilized for any DNA template; however, it is especially suited for primer design for chemically modified DNA used to determine the CpG methylation profile of a DNA template by the bisulfite genomic sequencing technique.
Designs primers optimized for whole genome polymerase chain reaction (PCR) scanning. GenoFrag was designed to allow a broad range of parameter implementations. It can be used for viral genomes, after a simple implementation to convert retroviral sequences. This application could also be implemented to generate primers to fill in the gaps between contigs in unfinished genome sequencing projects.
Assists molecular biologists in automating design of primers. AMUSER is a cloning method that enables advanced options for site-directed mutagenesis at multiple sites, introduction of degenerate nucleotides and construction of single insert combinatorial libraries by strategic design of specific USER cloning primers. It allows the user to submit DNA engineering queries in a simple Web interface and have the molecular details of the experiment automatically prepared.
Automates primer design for a number of well-defined genomic sequences. SNPbox offers a modular strategy for highly automated and standardized primer design in the construction of high-density single nucleotide polymorphisms (SNP) maps and mutation analysis based on resequencing of target sequences. It holds three modules for automated primer design: an SNP module, an exon module and a saturation module.
A web application for primer designs of DNA sequence PCR assembly. Primerize is optimized to reduce primer boundaries mispriming, is designed for fixed sequences of RNA problems, and passed wide and stringent tests. This efficient algorithm is suitable for extended use such as massively parallel mutagenesis library.
A computer program created to automate the design of oligodeoxynucleotides for the PCR-based construction of long DNA molecules. This program has been specifically designed to aid in the construction of DNA molecules that are to be used for the production of RNA molecules by in vitro synthesis with T7 RNA polymerase. The input for Assembly PCR Oligo Maker is either the desired DNA sequence to be made or an RNA sequence.
Evaluates a multiple alignment of phylogenetically related DNA sequences. PriFi is a web-based primer finder that suggests pairs of primers located in highly conserved regions. Two modes are provided: (i) the intron mode that requires all primer pairs to span at least one intron, and (ii) the general mode that expects no intron symbols in the sequences, and all criteria regarding introns become void.
Allows retrieval and assembly of gene sequences, and design of sets of primer pairs for gene amplification. GST-PRIME enables users to design a large numbers of primer pairs starting from a list of protein accession numbers. The software is able to detect and avoid introns and splicing sites during the primer design subroutine. It can be used for the amplification from both cDNA and genomic DNA. Representative sets of protein accessions from Arabidopsis thaliana and Drosophila melanogaster were used to test GST-PRIME.
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.
Allows simple sequence repeats (SSR) discovery and locus development from 454-generated raw data. HighSSR is a microsatellite prediction framework that can facilitate: the recognition of SSR motifs, the parsing of multiplex identifier (MID) tagged sequences for identification of multiplexed samples, the identification of unique SSR loci within a sample and the development of polymerase chain reaction (PCR) primers for the recovered loci. It can be applied to cluster reads made with platforms such as Illumina HiSeq 2000/2500 and Ion Torrent PGM.
Allows synthesis of large libraries of desired mutants across design and efficient organization of primers. The Primerize interface has been developed for RNA domains. This tool supports online design of primers and their organization into 96-well plates for M2 and M2 R studies. It supports M2 plates that enable separate synthesis of RNA single mutants for ‘two-dimensional’ data sets. User can submit his/her work if he/she provides the DNA template sequence.
Computes oligonuceotide primer pairs for genome-scale gene amplification by the polymerase chain reaction (PCR). PrimeArray executes the process of primer pairs via iteratively shifting primer candidates along the sequence. It uses melting temperature, GC-content and absence of unfavourable self- and primer–primer interactions to complete the process. This software allows users to customize tag sequences attached to the primer candidates.
Permits genome-wide investigation of microsatellites. Krait employs Primer3 as primer design engine to create amplification primers for identified microsatellite markers. It returns primer sequences and detailed information. This tool is applicable to a large number of microsatellites. It is able to identify the region where microsatellites are located thanks to utilization of GFF or GTF files.
Designs site-directed mutagenesis (SDM) primers. SDM-Assist is a standalone software that features the inclusion of a “silent” restriction site and a scoring algorithm for output primers. It fully supports drag and drop functionality and is well suited for touch-screen based devices. It consists of multiple steps: (i) introducing a mutation, (ii) restriction site search and replace, (iii) insertion of restriction sites and (iv) scoring.
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 several tools for microarray-based bacterial identification on short segments of DNA. Oligo Design offers as features: (1) dual sequence manipulation windows for one-click sequence manipulation, (2) automatic primer and oligoprobe design, (3) hairpin and self-annealing analysis, (4) analysis of given primer set against a target sequence and (5) analysis of a multiple alignment for universal primer sites and unique oligoprobes.
Predicts microsatellite molecular marker development. WebSat permits to submit sequences, and visualize microsatellites. It allows user to amplify and export the resulting data thank to design of primers suitable. The tool does not support large data sets. It returns the sequence identification, Simple sequence repeats (SSR), the product size, forward and reverse primer sequence, melting temperature, and coordinates of the primers within the sequence.
Permits to design degenerate primers. DePiCt starts by computing a sequence alignment of the genes or the protein sequences and then identifies at least two conserved regions in the alignment such that the target region to be amplified is contained in between them. It is able to quantify the similarity between aligned sequences. The tool uses nucleotide sequence alignment to decrease the degeneracy.
Detects short sequence repeats (SSR) and designs primers. FullSSR can detect all SSRs within a group of sequences and design primers for each SSR detected. The software simplifies the detection of SSRs and primer design on a big data set and provides results easily interpretable for nonexpert users. It was designed to be used as part of genomic analysis tools pipeline but can also be used as a stand-alone program.
Allows scientists to design, share, and record experiments or tests. The Benchling platform contains a Biological Registration System, an Electronic Lab Notebook, and Molecular Biology Design and Analysis Suite. This platform is made for scientists from pharma and biotech companies like government or academic labs. It permits users to share projects with co-worker and to control access to these projects.