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

1. Launch DNASIS MAX and import the Tutorial1.fsa file which is located in the
C:\HSK_DB\TutorialData directory.

Fig1. After loading the tutorial data.

2. Click the DNA – Compare tab and select the Internet – Blast Search option.

Fig2. DNA – Compare tag.

3. The Analysis dialog will appear.

Fig3. Analysis Dialog – In the Analysis Dialog, you will find the Parameter and Execute buttons.
The Parameter button is used for changing the parameters of an analysis.

4. Press the Parameter button and a dialog box will appear.
NCBI BLAST is set as the default URL.

Fig4. Internet Blast Search Parameterset dialog box.

5. Press the Setting… button to edit the parameters of NCBI BLAST.

Fig5.　NCBI Advanced BLAST Search dialog.

6. Once the configurations have been set, press the OK button.
To discard any changes, press the Cancel button.

7. Press the Execute button to send the query.
The time it takes to retrieve your results will depend on the size of the sequence, the database, and your internet service provider.  Once your results come back, it will be displayed like in Fig6.

Fig6. A sample result of the BLAST search in DNASIS MAX.

1. Launch DNASIS MAX and import the Tutorial1.fsa file which is located in the
C:\HSK_DB\TutorialData directory.

Fig1. After loading the tutorial data.

2. Click the DNA - Compare tab and select the Blast Search option.

Fig2. DNA – Compare tag.

3. The Analysis dialog will appear.

Fig3. Analysis Dialog – In the Analysis Dialog, you will find the Parameter and Execute buttons.
The Parameter button is for changing the parameters of an analysis.

4. Press the Parameter button and a dialog box will appear.

Fig4. BlastParameters dialog box.

5. Select the Blast program type from the Program name box.

• blastp – compares an amino acid query sequence against a protein sequence database
• blastn – compares a nucleotide query sequence against a nucleotide sequence database
• blastx – compares a nucleotide query sequence translated in all reading frames against a protein sequence database
• tblastn – compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames
• tblastx – compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

6. Set the E-value or Expect value in the Expectation value field. This value represents the number of times you would expect to see such a match (or better) merely by chance. The closer the value is to zero, the less likely the event is. To re-iterate, the smaller the E-value, the more significant the match is and the lower number of hits you’ll see.  The default value is 10.

7. Select the intended database from the Nucleotide Database.
Select the In-house-NA for this tutorial.

8. Once the configurations have been set, press the OK button.
To discard any changes, press the Cancel button.

9. Press the Execute button to start the blast analysis.

Fig5. A sample result of the Blast search in DNASIS MAX.

For more information on DNASIS MAX, please visit the DNASIS MAX product page or download the FREE trial.

1. Launch DNASIS MAX and import the Tutorial1.fsa file which is located in the

C:\HSK_DB\TutorialData directory.

Fig1. After loading the tutorial data.

2. Click the DNA – Search tab and select the Primer Design option.

Fig2. DNA – Search tab.

3. The Analysis dialog will appear.

Fig3. Analysis Dialog – In the Analysis Dialog, there are the Parameter and Execute buttons.  The Parameter button is for changing the parameters of an analysis.

4. Press the Parameter button and a dialog box will appear.

Fig4. PrimerParameterEditor dialog box.

5. Once the configurations have been set, press the OK button.
To discard any changes, press the Cancel button.

6. Press the Execute button to start the primer design.

Fig5. A sample result of primer design in DNASIS MAX.

For more information on DNASIS MAX, please visit the DNASIS MAX product page or download the FREE trial.

What can SmartNote offer to you?

• SmartNote has many analysis tools including popular tools such as Blast, ClustalW, Primer3 and much much more. You can run a single analysis on one sequence or save time by running a batch analysis on multiple sequences. If you don’t see a tool that you would like, then just request it and we will try our best to add it as soon as we can.
• You can easily share sequences, results, pages, and even your entire notebook with colleagues.
• Store and organize your sequences using our tagging system to find them easily later on.
• Track articles for your sequences. Do you find yourself constantly looking for new articles related to the sequences you are working on? Now, you can sit back and relax and let SmartNote automatically do it for you.

We are only skimming the surface here. If you are interested in the full potential of SmartNote and what it can do for you, then check it out for yourself!

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!