Get your free SmartNote online lab notebook

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?

Continue reading

LinkedInShare

DNASIS SmartNote Gets More Social (and now imports SNPs)

We’ve added a new “Friends” tab to make it easier to invite friends and colleagues to use DNASIS SmartNote. There are two options:

1 – Invite Friends – This is just an easy way to tell your friends and colleagues about DNASIS SmartNote, because every molecular biologist should be using it. :-)

2 – Invite and Share Notebook with Friends – This lets you not just invite friends to get their own account, but also to share their notebook and sequences with you. If they agree, you’ll be able to collaborate in cool new ways. First, you’ll be able to see read-only views of each other’s notebooks, which will appear below your own notebook navigator in DNASIS SmartNote’s left pane. Second, you’ll also be able to easily view or import each other’s sequences. You can then run your own analyses on your friend’s sequences. How cool is that?

On a separate “note”, we’ve added a new option under the “Sequences” tab for importing SNP sequences from NCBI. You can either search by keyword or by accession number. Enjoy!

LinkedInShare

Several Improvements to DNASIS SmartNote This Week

1. A job queuing system was implemented – You no longer need to wait for compute-intensive results (e.g. BLAST searches on multiple sequences) to come back. Just submit a job and continue working. When the results are in, you’ll be notified.

2. You can now add comments to tools and read other users’ comments. See what your colleagues have to say about which tools are best for a given task, or if there’s any tips and tricks to get the most value from a tool.

3. Auto-scrolling to results has been fixed – When you click on a result in the left pane, the right pane will automatically scroll to the corresponding position on the page so you can instantly access any result.

4. More help features to guide new users – You’ll notice several new icons to help you use SmartNote’s features.

5. Other cool additions such as the new animated progress icon for the sequence manager window.

6. Many bug fixes – everything just works more smoothly.

Remember to tell us what you think about DNASIS SmartNote and what new features you’d like to see. We’ve been making changes weekly, so as long as your request is reasonable, we’ll most likely be able to add it.

LinkedInShare

Tracking Articles Related to Your Sequences

By default, DNASIS SmartNote will track PubMed articles related to up to 10 of your most recently imported sequences. You can view these regularly updated articles by clicking on the “Articles” tab. From here, you can also clip individual articles into your notebook, as well as print and email them.

If you want to receive regular email updates for new articles, you’ll need to explicitly mark at least one of your sequences listed in the “My Seq’s” tab. You will then start receiving regular emails with any newly published articles related to your sequences. Since you can only track 10 sequences, the sequences you have explicitly marked will get higher priority.

How does DNASIS SmartNote find related articles? If the sequence was imported as a GenBank file, DNASIS SmartNote looks for gene names in the annotations. Otherwise, it defaults to a plain text search of words in the sequence’s description.

We invite you to try out this new feature and let us know if we can do anything to improve it for you.

LinkedInShare

10 Tips For Designing PCR Primers That Work

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/

LinkedInShare

Track articles related to your sequences and congrats to Boris Zinshteyn!

DNASIS SmartNote now tracks articles related to your sequences as they are published. You can see a list of recent articles relevant to all your sequences by clicking the “Articles” tab at the top, or click the “Related articles” link next to each sequence to see only articles for that sequence. Coming soon – you’ll be able to clip individual articles into your lab notebook!

Congratulations to Boris Zinshteyn for winning the Top Feedback prize of a $25 Amazon.com gift certificate! We still have plenty of gift certificates available, so please take a couple of minutes to tell us what you think about DNASIS SmartNote and especially how we can improve it for you.

LinkedInShare

Share sequences with colleagues, export sequences in FASTA, and winners of our Feedback contest

Congratulations to James Galen and Jessica Min for winning the Top Feedback contest for $25 Amazon.com gift certificates. We value our user’s input as it helps make the application better for everyone.

New this week:

1. You can now share sequences with colleagues via the new Friend’s Sequences tab. This will allow you to easily view or copy any sequence from anyone in your friends list.

2. Do you need to export your sequences? A new feature has been added that will export your sequences in FASTA format. If you have multiple sequences selected, they will all be in a single file in multi-FASTA format.

The Top Feedback contest is still going so please take a minute or two and tell us about your experience with SmartNote.

LinkedInShare

Export/print results, new PrimerX tool, invite GMail + Yahoo Mail contacts and more!

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!

LinkedInShare

Import GenBank files, new translation view and IUPAC codes

New this week:

1. By popular demand, you can now import GenBank and multi-GenBank files into SmartNote, including those exported from other programs, such as DNASIS Max and Vector NTI.

2. We have added a new option for displaying the predicted amino acid sequence aligned with a DNA sequence. Use the ExPASy Translate tool and specify “Includes Nucleotide Sequence” for the “Output Format” option. Thank you, Jessica Min for this suggestion. This should help users who need to design primers for mutagenesis.

3. Support for IUPAC codes in sequences is also being added this week.

Please keep the feedback coming!

LinkedInShare