The MiraiBio Group Blog » blast search

How to run an Internet Blast search with DNASIS MAX

kokubo — Mon, 11 Aug 2008 17:23:43 +0000

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.

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.

How to run a Blast search with DNASIS MAX

kokubo — Mon, 23 Jun 2008 16:14:44 +0000

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.

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.

Several Improvements to DNASIS SmartNote This Week

Allen Liu — Mon, 31 Mar 2008 21:57:53 +0000

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.