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Primer design software tools | Synthetic biology

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…
Primerize-2D
Web

Primerize-2D

Allows synthesis of large libraries of desired mutants across design and…

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…

G T A T C G C T A
Krait
Desktop

Krait

Permits genome-wide investigation of microsatellites. Krait employs Primer3 as…

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…

Primerize
Desktop
Web

Primerize

A web application for primer designs of DNA sequence PCR assembly. Primerize is…

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…

AMUSER
Web

AMUSER Automated DNA Modifications with USER cloning

Assists molecular biologists in automating design of primers. AMUSER is a…

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…

Assembly PCR…
Desktop

Assembly PCR Oligo Maker

A computer program created to automate the design of oligodeoxynucleotides for…

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…

BiSearch
Web

BiSearch

Provides a web server to design for the amplification of single templates.…

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…

GenoFrag
Desktop

GenoFrag

Designs primers optimized for whole genome polymerase chain reaction (PCR)…

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…

PrimerSNP
Web

PrimerSNP

Automates selection of specific primers that contain strain-specific single…

Automates selection of specific primers that contain strain-specific single nucleotide polymorphisms (SNPs) at the genome level. PrimerSNP identifies primers that can be used to reliably…

SDM-Assist
Desktop

SDM-Assist

Designs site-directed mutagenesis (SDM) primers. SDM-Assist is a standalone…

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…

GST-PRIME
Desktop

GST-PRIME

Allows retrieval and assembly of gene sequences, and design of sets of primer…

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…

Sequence…
Web
Desktop

Sequence Extractor

Provides a clickable restriction map and polymerase chain reaction (PCR) primer…

Provides a clickable restriction map and polymerase chain reaction (PCR) primer map of a DNA sequence. Sequence Extractor is a web application that was developed to build in silico DNA constructs. It…

PrimerX
Web

PrimerX

Automates the design of mutagenic polymerase chain reaction (PCR) primers for…

Automates the design of mutagenic polymerase chain reaction (PCR) primers for site-directed mutagenesis. PrimerX works in 4 steps: It (i) compares a template DNA sequence with a DNA or protein…

PrimerPipeline
Desktop

PrimerPipeline

Serves for microsatellite mining. PrimerPipeline is a program also dedicated to…

Serves for microsatellite mining. PrimerPipeline is a program also dedicated to primer design for de novo low coverage genomes. It allows users to search microsatellites and to design primers. It can…

Collagene
Desktop

Collagene

Supports and allows reutilization of contemporary cloning methods. Collagene…

Supports and allows reutilization of contemporary cloning methods. Collagene offers advanced functions for the visualization of the results.

G T A T C G C T A
WebDSV
Web

WebDSV

Allows users to work on DNA sequences. WebDSV assists in creation, edition and…

Allows users to work on DNA sequences. WebDSV assists in creation, edition and analysis of DNA sequences. This tool enables visualization of sequences and permits user to mark them. It generates…

DePiCt
Web

DePiCt

Permits to design degenerate primers. DePiCt starts by computing a 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…

Benchling
Web

Benchling

Allows scientists to design, share, and record experiments or tests. The…

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…

MutScreener
Web

MutScreener

Provides comprehensive functions for Polymerase Chain Reaction (PCR)-sequencing…

Provides comprehensive functions for Polymerase Chain Reaction (PCR)-sequencing assay design. MutScreener offers multiple choices of inputs including cDNA IDs, cDNA sequences, DNannotator annotated…

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