MasterPlex QT is a multiplex expression data analysis software for those looking for normalization or fold change calculations.   Our flash demo tutorial covers the following topics:

• Marking and grouping wells
• Linking treatment to control groups
• Assigning the housekeeping gene(s)
• Calculating the normalized and fold change values

View the tutorial and find out how easy analysis can be!

In an effort to make standard curve fitting even easier and add more value to MasterPlex we have included a Best Fit feature in the latest version of QT. After importing your xMAP/BioPlex data and applying your analysis template you can select the Best Fit feature. The software will automatically cycle through the myriad of standard curve fit choices and select the best model equation and weighting algorithm for EACH analyte.

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MiraiBio has heard your voice and we realize that not all customers require a perpetual license when there is only the need to use our Luminex analysis software a couple of times a year.

We are now happy to introduce the new Term Licensing options for our MasterPlex QT and GT Luminex data analysis software.  Term Licensing durations include the 3, 4, 5, 6, 7, 8, 12, or 24 month options.  The software license expires at the end of the purchased term and also includes all major upgrades released during the term.

For those that do not need to run analyses 24/7, this may be the cost-efficient choice for you.  To find out more details, please visit the MasterPlex QT product page or the MasterPlex GT product page at the MiraiBio Store.

DNASIS MAX has the ability to search for homologous sequences to your sequence with BLAST (Basic Local Alignment Search Tool). BLAST finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

The following procedure guides you through utilizing BLAST against NCBI’s sequence databases.

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Many of the FlexMAP (now called xTAG) microsphere users relied on the TagIT software to help choose which microsphere sets to use in genetic detection assays run on the xMAP platform. When the TagIT software was removed these users no longer had a reliable way to design their assays. Well the good news is that TagIT is back!

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DNASIS MAX has the ability to search for homologous sequences to your sequence with Blast which is
useful in judging if the sequence is novel or even add annotations from known gene information. The following procedure guides you through utilizing Blast against an internal sequence database.

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DNASIS MAX uses the Primer3 engine for designing primers, which is one of the most frequently used procedures in daily research.  The following procedure guides you through designing primers utilizing the DNASIS MAX interface.

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We have cataloged and placed many custom report templates for our MasterPlex QT 2.5/3.0 customers to download and use. These templates are to be used in conjunction with the Custom Report Generator in MasterPlex QT. Click on the Details button for each report to view a screenshot of a sample report generated using the template file.

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MiraiBio has gone online with software. We are pleased to introduce a revolutionary way to store and analyze your sequences and share them with colleagues.

What can SmartNote offer to you?

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Since PCR primer design is one of the most widely used features of DNASIS SmartNote, we did some research and put together a list of the top 10 tips for designing PCR primers that work. When designing oligonucleotide primers for PCR, it is helpful to keep some considerations in mind to optimize the output and specificity of your experiment. Here are some tips gathered from experts to get you started:

1. Design your PCR primers to be 18-30 oligo nucleotides in length. The longer end of this range allows higher specificity and gives you space to add restriction enzyme sites to the primer end for cloning.

2. Make sure the melting temperature (Tm) of the primers used are not more than 5°C different from each other. You can calculate Tm with this formula: Tm = 4(G + C) + 2(A + T)°C

3. Aim for a Tm between 65 and 70°C for each primer over the region of hybridization

4. Use an annealing temperature (Ta) of 10 to 15°C lower than the Tm.

5. The GC content of each primer should be in the range of 40-60% for optimum PCR efficiency.

6. Try to have uniform distribution of G and C nucleotides, as clusters of G’s or C’s can cause non-specific priming.

7. Avoid long runs of the same nucleotide.

8. Check that primers are not self-complementary or complementary to the other primer in the reaction mixture, as this will encourage formation of hairpins and primer dimers and will compete with the template for the use of primer and reagent.

9. If you can, make the 3′ end terminate in C or A, as the 3′ is the end which extends and neither the C or A nucleotide wobbles. This will increases the specificity.

10. You can avoid mispriming by making the 3′ end slightly AT rich.

11. Use the right software. OK, so it’s 11 tips. Using the right software is a great way to automate these steps and minimize errors, especially when you have to design primers for many sequences. DNASIS SmartNote includes several primer design tools and is also a lab notebook that automatically keeps a record of your analysis results. You should definitely give it a try. Click here to sign up a free account.

If you prefer traditional desktop software, take a look at DNASIS Max instead.

References:

http://rothlab.ucdavis.edu/protocols/PrimerDesign.html

http://www.biochem.ucl.ac.uk/bsm/nmr/protocols/protocols/oligo.html

http://www.protocol-online.org/prot/Molecular_Biology/PCR/PCR_Primer/

http://www.mcb.uct.ac.za//pcroptim.htm

New this week:

1. You can now export individual results (summaries or raw) from your lab notebook as PDF files or print them out.

2. The PrimerX tool has been added to support primer design for mutagenesis. It even works with multiple sequences!

3. You can now extract email addresses from your GMail or Yahoo mail accounts to make it easier to invite your colleagues to collaborate with you through DNASIS SmartNote.

4. If you find yourself using the same tools frequently, you’ll love this feature: when it’s time to pick a tool for an analysis, you can now see the 5 most recently used tools listed at the very top and just click them to quickly launch the analysis.

Coming soon… an exciting new way to share data with colleagues!

DNASIS SmartNote was recently released to a limited group of scientists and attracted some great feedback. Here’s a quick summary:

Some users said they needed more help getting started using it. This is not surprising, since DNASIS SmartNote’s design is innovative in two ways – it’s a meta-application (an application that uses other applications) and it’s also the first bioinformatics tool we know of that combines a lab notebook, sequence analysis and social networking.

Others said they want to be able to import sequences in formats other than FASTA. I’m happy to report that GenBank support will soon be available on the live site.

Finally, we are starting to get requests to support specific workflows, such as designing primers for mutagenesis. One user suggested adding a view that shows both DNA and protein sequences. We would love to hear from other DNASIS SmartNote users so we know where to focus our efforts to best meet users’ needs. So please send us feedback or post to this shared blog. Together, we can make DNASIS SmartNote even better!