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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 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.

Source text:
(Tian et al., 2015) Primerize: automated primer assembly for transcribing non-coding RNA domains. Nucleic Acids Res.

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AMUSER / Automated DNA Modifications with USER cloning
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.
GST-PRIME
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.
PrimerX
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 sequence, (ii) generates forward primer sequences by computing for all possible oligonucleotide sequences of appropriate length, (iii) generates corresponding reverse primer sequences, and (iv) computes for other necessary information such as melting temperature and GC content for each primer pair.
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