• New Exon Primer tool for alternative splicing analysis
  
  
• Primer Design, Multiple Alignment and Blast tools updated for better accuracy
• Improved Custom Database Management
  
  
• Windows 7 compatibility

Visit the DNASIS MAX v3.0 product page for more information or Download the 14-day Free Trial.

Adaptive Evolution in Rodent Seminal Vesicle Secretion Proteins
Robert Karn et al.
Molecular Biology and Evolution 25 (11), (01 Nov 2008)
http://mbe.oxfordjournals.org/cgi/content/abstract/25/11/2301
PMID:18718917
doi:10.1093/molbev/msn182

Molecular characterization of the hemagglutinin-neuraminidase gene of porcine rubulavirus isolates associated with neurological disorders in fattening and adult pigs.
J I Sánchez-Betancourt et al.
Research in veterinary science 85 (2), 359-67 (Oct 2008)
http://www.ncbi.nlm.nih.gov/pubmed/18031776
PMID:18031776
doi:10.1016/j.rvsc.2007.10.007

Molecular detection and characterization of unclassified bovine enteric caliciviruses in South Korea.
Sang-Ik Park et al.
Veterinary microbiology 130 (3-4), 371-9 (25 Aug 2008)
http://www.ncbi.nlm.nih.gov/pubmed/18387758
PMID:18387758
doi:10.1016/j.vetmic.2008.01.017

The role of polymorphisms at beta tubulin isotype 1 codons 167 and 200 in benzimidazole resistance in cyathostomins.
J E Hodgkinson et al.
International journal for parasitology 38 (10), 1149-60 (Aug 2008)
http://www.ncbi.nlm.nih.gov/pubmed/18367189
PMID:18367189
doi:10.1016/j.ijpara.2008.02.001

Identification of Armillaria nabsnona in gastrodia tubers.
Haruo Sekizaki et al.
Biological & pharmaceutical bulletin 31 (7), 1410-4 (Jul 2008)
http://www.ncbi.nlm.nih.gov/pubmed/18591784
PMID:18591784

Dissection of the clonal composition of bovine alphabeta T cell responses using T cell receptor Vbeta subfamily-specific PCR and heteroduplex analysis.
T Connelley et al.
Journal of immunological methods 335 (1-2), 28-40 (01 Jun 2008)
http://www.ncbi.nlm.nih.gov/pubmed/18436232
PMID:18436232
doi:10.1016/j.jim.2008.02.015

Diagnostic accuracy of class 1 integron PCR method in detection of antibiotic resistance in Salmonella isolates from swine production systems.
Sangeeta Rao et al.
Journal of clinical microbiology 46 (3), 916-20 (Mar 2008)
http://www.ncbi.nlm.nih.gov/pubmed/18174294
PMID:18174294
doi:10.1128/JCM.01597-07

Genetic classification and distinguishing of Staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences.
B Ghebremedhin et al.
Journal of clinical microbiology 46 (3), 1019-25 (Mar 2008)
http://www.ncbi.nlm.nih.gov/pubmed/18174295
PMID:18174295
doi:10.1128/JCM.02058-07

Hematologic, cytochemical, ultrastructural, and molecular findings of Hepatozoon-infected flat-headed cats (Prionailurus planiceps).
Chaleow Salakij et al.
Veterinary clinical pathology / American Society for Veterinary Clinical Pathology 37 (1), 31-41 (Mar 2008)
http://www.ncbi.nlm.nih.gov/pubmed/18366542
PMID:18366542
doi:10.1111/j.1939-165X.2008.00011.x

Detection of hepatitis E virus (HEV) in a demographic managed wild boar (Sus scrofa scrofa) population in Italy.
Francesca Martelli et al.
Veterinary microbiology 126 (1-3), 74-81 (01 Jan 2008)
http://www.ncbi.nlm.nih.gov/pubmed/17706898
PMID:17706898
doi:10.1016/j.vetmic.2007.07.004

Molecular cloning and characterization of prostaglandin (PG) transporter in ovine endometrium: role for multiple cell signaling pathways in transport of PGF2alpha.
S K Banu et al.
Endocrinology 149 (1), 219-31 (Jan 2008)
http://www.ncbi.nlm.nih.gov/pubmed/17901226
PMID:17901226
doi:10.1210/en.2007-1087

Molecular epidemiology of bovine toroviruses circulating in South Korea.
Su-Jin Park et al.
Veterinary microbiology 126 (4), 364-71 (25 Jan 2008)
http://www.ncbi.nlm.nih.gov/pubmed/17719729
PMID:17719729
doi:10.1016/j.vetmic.2007.07.012

Reliable identification of mycobacterial species by PCR-restriction enzyme analysis (PRA)-hsp65 in a reference laboratory and elaboration of a sequence-based extended algorithm of PRA-hsp65 patterns.
Erica Chimara et al.
BMC microbiology 8, 48 (2008)
http://www.ncbi.nlm.nih.gov/pubmed/18366704
PMID:18366704
doi:10.1186/1471-2180-8-48

Molecular characterization of composite mantle cell and follicular lymphoma.
Alberto Zamò et al.
Virchows Archiv : an international journal of pathology 448 (5), 639-43 (May 2006)
http://www.ncbi.nlm.nih.gov/pubmed/16491375
PMID:16491375
doi:10.1007/s00428-006-0158-9

The zebrafish kohtalo/trap230 gene is required for the development of the brain, neural crest, and pronephric kidney.
Sung-Kook Hong et al.
Proceedings of the National Academy of Sciences of the United States of America 102 (51), 18473-8 (20 Dec 2005)
http://www.ncbi.nlm.nih.gov/pubmed/16344459
PMID:16344459
doi:10.1073/pnas.0509457102

Nanomolar aluminum induces pro-inflammatory and pro-apoptotic gene expression in human brain cells in primary culture.
Walter J Lukiw, Maire E Percy, and Theo P Kruck
Journal of inorganic biochemistry 99 (9), 1895-8 (Sep 2005)
http://www.ncbi.nlm.nih.gov/pubmed/15961160
PMID:15961160
doi:10.1016/j.jinorgbio.2005.04.021

Molecular analysis of S gene of spike glycoprotein of winter dysentery bovine coronavirus circulated in Korea during 2002-2003.
Jae-Ho Jeong et al.
Virus research 108 (1-2), 207-12 (Mar 2005)
http://www.ncbi.nlm.nih.gov/pubmed/15681072
PMID:15681072
doi:10.1016/j.virusres.2004.07.003

Can DNASIS MAX help you?

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.

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!