![]() This could be a very good resource for someone starting out in qPCR. The page also has handy dilution and resuspension calculators to help you with the dreaded task (for me anyway!) of preparing your working primer solutions. You can calculate the general properties of primers and amplicons as well as design highly customized oligos depending on your specific needs. The majority of molecular biologists I know swear by Serial Cloner J.Īlthough not exclusively a PCR website, you can find a lot of very useful tools here to help you plan your PCR and Real-Time PCR experiments. You can also use Serial Cloner to prepare plasmid maps and diagrams of cloning setups to help in your presentations and reports. Once you’ve installed the program and saved your DNA and primer sequences you can run hypothetical PCRs, view restriction sites, and perform test digests (you can even add your molecular weight marker to get an idea of how your agarose gel should look!), carry out sequence alignments, plan gateway cloning experiments, and much more. Serial Cloner can be downloaded as freeware for Mac and Windows OS and is definitely worth having if you carry out PCR and cloning on a regular basis. Of course, if you are amplifying your target from a plasmid, the risk of unspecific PCR products will be lower. National Centre for Biotechnology Information (NCBI)ĭid you know that the NCBI website can be used for so much more than literature and BLAST searches? At primer blast you can search for suitable primer pairs (much like Primer3), or you can enter specific primer sequences and check their specificity by performing a primer blast, helping you to avoid off-target amplification. BLASTing your primers against your genome of interest might be particularly useful if you are trying to amplify a gene that exists as part of a multigene family if your template is total genomic DNA. You can also use Primer3 to design hybridization probes for use in PCR-ELISA and other probe-based applications.Ģ. You can choose to refine your results in several ways, including the size of your desired PCR product, primer size, Tm range, and other parameters. You simply paste in your target sequence and search for primers. Primer3 is a very simple yet efficient online interface for primer design. Looking for new PCR reagents and equipment.Estimating PCR efficiency from the slope of an amplification curve so you don’t need to run standard curves in qPCR.Relative gene expression analysis for your raw qPCR data.Restriction mapping of your PCR product to aid cloning.Calculating general properties of primers and amplicons (Tm, secondary structure, primer dimers).How do you sort out the > 20 million hits you get when you Google ‘PCR’? This list of the Top 10 PCR websites contains those used by myself and colleagues and should be a good go-to for any of the following PCR issues: In conclusion, Serial Cloner is a very user-friendly and powerful Molecular biology tool.Whether you are embarking on a PhD in molecular biology, trying to amplify a new gene, analyzing gene expression by qPCR, or trying to solve a PCR problem, you will probably resort to a Google search at some point or another. Fragments obtained by PCR, shRNA synthesis, can be easily assembled by selecting between the restriction sites.We can also ligate fragments using the ligate button.Also, to create new PCR based fragments or synthetic adaptors. We can use either the graphics window or the text-based site usage windows, which makes it very easy to quickly extract a sub-sequence in a selection or in any restriction sites.There is a web browser tool within the software to allow direct import of NCBI and EMBL.Sequence features are visible on the sequence map.They can be automatically found by using the scan feature. Features can be manually entered or imported.The fully graphical map makes it easy to extract and select a fragment or even show single, double, or multiple cutters in a single window.All the tools required to analyze the sequence and modify if any changes needed are available in a single window making it very easy to use.The software comes with a high-quality graphics display and has a very user-friendly interface to the front end, which makes the interface very intuitive. They are processed both in sequence and as a graphic map. ![]() Since version 2.0 of the software, it also handles Annotations and features. It can read and write files in several formats, making it portable across multiple users who use different Molecular Biology tools. It is available free for download and can be used across multiple Operating Systems, including Windows, Mac, and Linux. Serial Cloner is a Molecular Biology Tool which is a front end to help with DNA Cloning, Sequence Analysis, and Visualization. ![]()
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