Version History

6.4.0 (May 12, 2008)

Improvements/new features:

1. Addition of Peptide Nucleic Acid (PNA)/DNA parameters. This is based on hundreds of measurements made at DNA Software. The Tm is predicted within 2 °C, on average.
2. Addition of the modified nucleotide Deoxyuracil in DNA duplexes. This accounts for the thermodynamic differences of dT and dU in DNA with a full nearest neighbor model that gives Tm predictions within 2 °C, on average. This allows users to design primers and probes for target amplicons made using dUTP, which is used to minimize contamination artifacts . This is also useful for designing assays for DNA deamination and methylation.
3. Expansion of sequences containing ambiguity codes. This facilitates the simulation of primers against SNPs that are designated in genomic sequences as amibiguity codes.
4. Many improvements to the DNA Display graphic such as inclusion of solution conditions and improvements to the cycling of suboptimal structure displays.
5. Improvements to various issues in Sequence Editor such as copying and pasting of sequences and sequence modifications.

Bug fixes:

1. Improved Numerical Analysis Graph displaying heterodimer in Graph Key.
2. Fixed Restoring Factory settings causing error in Visual OMP.
3. Fixed betaine sequence null error when viewing sequences tab.

6.3.0 (February 22, 2008)

Improvements/new features:

1. Betaine Monohydrate (PCR Buffer additive) Free Energy Correction.
2. Bulk Edit function to simultaneously edit multiple sequence/design rows that can be used along with filter function to selectively edit multiple entries.
3. Filter function to selectively remove sequence/design rows for editing.
4. Restriction Enzyme Function to simulate restriction fragments in silico.
5. Duplex Polymer Salt Correction is defaulted to be always on for more accurate Free Energy Corrections for oligonucleotide designs > 16 nucleotides.

Bug fixes:

1. Improved memory management for Scorpion designs.
2. The equilibrium constants were not set equally for some heterodimer cases.

6.2.2 (August 2, 2007)

Improvements/new features:

1. TMAC correction implemented (15 mM - 4.1 M)
2. European number format compatible
3. new icon to show/hide advanced parameters on the probe/primer design tab
4. new icons for NumAnaly graph (same functionality as right-click context menu)
5. warning message when entering inconsistent values for advanced parameters
6. remember custom project folder where new projects are created through the Wizard
7. size of forms of existing experiments is saved for future opening and size of forms of new experiments fit within window
8. advanced parameters grid automatically sized to not overlap design rows

Bug fixes:

1. Check for Updates regression Vista issue
2. various issues on the sequence view tab
3. hover box for Numerical Analysis graph with non-default Min Temperature
4. saving of disabled keywords for future use (Experiment Conditions and Structure Settings tabs)
5. opening scorpion design output when experiment grid itself is not open
6. illegal characters when pasted into Sequence Name field automatically filtered out
7. critical error when trying to open deleted project from wizard at start-up
8. splash screen when opening Visual OMP keeps the focus, so that it is not hidden behind Visual OMP in case other applications are opened simultaneously
9. error when saving experiment that contains empty Sequence fields
10. error when right-clicking on window that does not have the focus

6.1.9 (May 8, 2007)

1. Windows Vista compatible
2. Sorting the results summary for concentration is fixed
3. Lowercase IUPAC code in the Variation column (Sequences tab) is fixed
4. Biomolecular folding of sequences over 3,000 nucleotides is fixed
5. Intend = TRUE for both optimal + suboptimal structures on Results Summary is fixed
6. Visual OMP seeming busy after using Entrez search form is fixed
7. Errors when disabling/deleting targets which are referred to in a design are fixed
8. When a sequence is 100% random coil, this will now be displayed on the Results Summary
9. Warning when Blast is enabled, but no Blast database is selected on the Design Settings tab is implemented
10. Warning when a sequence contains over 25 variations is implemented
11. Warning when experiment contains 2 identical sequences of the same type is implemented
    
    

6.0.0 (December 15, 2006)

1. Inosine incorporation for all DNA-DNA match and mismatch parameters
2. Improved DNA-RNA mismatch (internal and terminal), dangling end, bulge, loop, and hairpin parameters
3. Improved DNA-RNA magnesium dependence
4. Check if sequences contain over 25 variations
5. Ability to force Visual OMP to simulate sequences over 3000 nucleotides long
6. Maximum allowed monovalent concentration increased from 1M to 1.1M
7. Hover menu over sequences also accounting for Inosine (purine) and Uracil (pyrimidine)
8. Copying of scorpion experiments
   

5.0.5 (May 15, 2006)

1. Scorpion closed stem error fixed
2. Scorpion custom strategies error fixed
3. BLAST exclude keywords error fixed
4. Wizard button added to menu
5. Scorpion closed stem maximum loop size default updated
6. Scorpion amplification boundaries check error fixed

5.0.2 (March 29, 2006)

1. OMPUtilities made available to OMP DE customers

5.0.1 (February 14, 2006)

1. Customized User Files Backed up in installation
2. SequenceEditor.ocx fixed
3. Updated Menu in StartUp Menu
4. Windows Registration Error fixed

5.0.0 (January 16, 2006)

1. New design type: Allele Specific PCR primers (ASPCR)
2. New design type: Scorpion primers (ARMS, ASO & QPCR, open or closed form)
3. Require Solutions: option to force Visual OMP to output solutions after a design run
4. Possibility to search the Entrez website through the Entrez Search form in Visual OMP; sequences are then easily added to experiments
5. New Variation-column on the Probe/Primer Design tab to accommodate ASPCR designs
6. Updated and improved default design strategies under the Strategy-column on the Probe/Primer design tab
7. Ability to reload older V 4.2.X design strategies
8. The help-files are updated with new screenshots and two new tutorials on ASPCR and Scorpion designs
9. AOI2Server contains versioning
10. Menu depth changed in design tab
11. Known Issues

    - Progress bar bug with Scorpion Design
    - Scorpion Design allowed with N variation
    - Sequence Editor sometimes causes tab selection to unnecessarily change to sequences tab
    - ASPCR does not work if single nucleotide is given as Amplification Window
    

4.2.2 (September 30, 2005)

1. Issues related to (multiplex) design of TaqMan (MGB) Probes fixed
2. Dynamic grid issues for TaqMan (MGB) Probe designs fixed
3. Error while using delete-key in Position/Range cell on Probe/Primer Design tab fixed; delete-key doesn't work in this cell for the moment
4. Error when saving an experiment that contains an open sequence view tab of a deleted sequence fixed
5. Crosshybridization grid not taking user to corresponding cell on Results Summary for certain structures fixed
6. New option "Locate Within Output" from the context menu on the Crosshybridization Grid (right-click) to take user to the corresponding cell on the Results Summary
7. Ignoring of Accession numbers, Genbank numbers and Keywords for Blast during design on the Design Settings tab simplified and fixed

    

4.2.1 (August 31, 2005)

1. Updated Modification Parameters
2. Updated DMSO Parameters
3. Sequence font changed to Courier to allow easier comparison
4. Beacon Stems can be forced to contain G/C terminal pair
5. Variations can be longer than 1 nucleotide - also now accept A/C/G/T/U as valid bases within variations
6. Min Numanaly and Max Numanaly bug fixed
7. Improved Model, temperature dependence and parameters for MGB TaqMan probes. Based in part on - Igor V. Kutyavin et al. “3’-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures.” Nucleic Acids Research, 2000, Vol. 28 No. 2.
8. Improved Fluorophore thermodynamic parameters. These are due to measurements made in our laboratory and based on the following papers:
   - Salvatore A. E. Marras, Fred Russell Kramer and Sanjay Tyagi. “Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes.” Nucleic Acids Research, 2002, Vol. 30 No. 21.
   - Bernardo G. Moreira, Yong You, Mark A. Behlke and Richard Owczarzy. “Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability.” Biochemical and Biophysical Research Communications, 2005, Vol. 327 No. 2.
9. Microarray Correction in the "Experiment Conditions Tab" - Alinear correction to solution thermodynamics that was shown by Fotin et al. to allow good agreement between solution predictions and experiments in microarrays that use gel pads. Note that there was a typo in the Fotin paper that we have corrected, which is the option "SantaLucia Correction"
10. Polymer Salt Correction. The 1998 paper by SantaLucia (SantaLucia, J. (1998) P.N.A.S. 95, 1460-1465) indicated that polymer duplexes (greater than 16 base pairs) have a different salt dependence than oligomers due to end effects and counterion condensation effects. The latest version of OMP provides a checkbox in the "Conditions Window" called the "Polymer Salt Correction". If this box is checked (which is recommended best practice), then the software applies the polymer salt correction to all duplexes that are longer than 16 Basepairs, while shorter duplexes and unimolecular folds are unaffected.
11. New DeltaCp Feature (change in heat capacity): There have been several reports in the literature (See references in the SantaLucia and Hicks review article) that at low temperature DNA single strands can form ordered structures (typically an ordered single strand helix or small hairpin). Thus, when a duplex melts at low temperature the unfolded state is not fully random, resulting in observed deltaG that is higher than expected (i.e. less stable) and resulting in apparent temperature dependent deltaH and deltaS (and smaller temperature dependence in deltaG due to enthalpy-entropy compensation). Our previous version of OMP already accounted for the multi-state competition of small hairpins (this is what percent bound and the Numerical Analysis did and still do). To account for the effect of single strand stacking, we have included a DeltaCp correction. The default value is set to "0.0", which makes no correction in thermodynamics. Note that we recommend a value of 0.05 kCal/mol K per basepair. This is somewhat smaller than the value of 0.1 that previous investigators have recommended to account for both single strand stacking and small hairpin formation because OMP already accounts for the small hairpins. The new DeltaCp correction provides for improved predictions at temperatures below 20 oC, makes very slight changes from 20 to 50 oC, and makes no change above 50 oC.
12. Bug fixes

    - RNA large hairpin bug. Previous versions of OMP would sometimes produce RNA secondary structures with very large hairpin loops - particularly at low salt and high temperature conditions. This was not really a bug, but was due to limitations in the sequence dependent hairpin model. We have significantly improved the RNA hairpin model so that it still predicts excellently at typical salt and temperature conditions, but now also works well at more extreme conditions. The new proprietary RNA parameters provide the best RNA secondary structure predictions available.
    - Now it is possible to fold a restricted part of a long sequence when using seq start and end cells.
    - A bug in multiplex probe pair design is fixed.
    - Recovering 2 custom strategies after they have been deleted is fixed.
    - Saving of N-plex and exclude target-target duplex settings.
    - From now on Visual OMP will warn users when illegal characters are used in the sequence name.
    - Error when right-clicking on results summary behind a DNA-display.
    - The Variation Position row will now be shown for all design types again.
    - Error when enabling/disabling sequences while sequence cell is highlighted.
    - It is not possible anymore to run designs when there is no sequence specified on the sequences tab.

13. Known issues we are working on

    - Variation Position parameter. Due to the not showing and saving of the Variation Position parameters in Visual OMP 4.1 (one of the advanced parameters on the Probe/Primer Design Tab), one will need to double-check this row when opening up designs made in a previous version of Visual OMP; on occasions it can be empty, usually default values will be filled out.
    - Reporting of amplicon size when designing a single forward or reverse primer; when no region to be amplified this is reported with respect to the 5’ end of the target (reverse primer) or 3’ end of the target (forward primer) which is incorrect.
    - The current version of OMP allows the user to input the same sequence more than once (and with different concentrations) in a single experiment. This is non-physical and the GUI will be enhanced in the next release to prevent the user from simulating such a system.
    

     

4.1.0 (April 15, 2005)

1. Updated Modification Parameters
2. Dual Modification Parameters
3. Beacons
4. Beacon Pairs
5. Automatic sorting of Advanced Parameters
6. Min Numanaly and Max Numanaly bug fixed

4.0.9 (January 26, 2005)

1. DMSO-correction updated
2. Double stranded RNA bug - fixed
3. Cross-hybridization grid bug linking to wrong cells on results summary - fixed
4. Location bug output files after moving of experiment - fixed
5. Issues with the text-editor - fixed

4.0.6 (December 13, 2004)

1. New tab added for more visualization: the sequence view tab
To view this tab, go to the sequence of interest on your sequences tab, click on the sequence column and the on the grey square box in the right corner of the cell. This tab will show the literal sequence at the bottom and (when simulated before) the secondary structure of the sequence on the right hand side. Several visualization options can be chosen on the left

2. Splitting up of settings tab into experiment conditions tab and design settings tab
This enhances transparency and separates simulation and design more. All settings on the experiment conditions tab are used both during simulations and design, whereas the settings on the design settings tab are only used during design.

3. New buffer options for the solution conditions
Apart from temperature and salt concentrations, the buffers glycerol, TMAC and formamide can now be used in the solution conditions.

4. New design options
It's now possible to design RNA probes and TaqMan probes.

5. Possibility to put modifications on sequences
Modifications can be added to both sequences on the sequences tab and sequences being designed on the probe/primer design tab.

6. Possibility to prevent unintended extensible structures while designing
On the design settings tab it can be indicated if primers/probes which are being designed and will cause certain extensible structures in the solution should be rejected.

3.2.7 (April 5, 2004)

1. Paste from EXCEL fixed.
2. Sorting (single and multiple) by column in any VO window fixed

3.2.6 (March 5, 2004)

1. BLAST: default word size is set to 11, matches to NCBI’s default setting
2. SETTINGS TAB: bug fixed - can now delete custom solutions
3. LICENSE: new license management
4. DESIGNS TAB – Fixed bugs:

a. Probe pairs can now be designed for insertions and deletions
b. Fixes in Q-score that had affected length and negative wt scores

3.2.5 (February 3, 2004)

Changes were at the OMP engine level.

1. Sequence-specific bug gave very high percents – fixed.
2. Sequence-specific bug for n-plex simulations gave too high dG, affecting percent bound – fixed.

3.2.3 (Dec 15, 2003)

1. New license management
2. Minimum solution distance bug fixed
3. Tailfolding energies are now incorporated in the heterodimer dG when tailfolding is set to on

You can now specify if the probes are DNA or RNA by adding keywords (in DE)
OLIGO_SEQUENCE_TYPE=DNA
OR
OLIGO_SEQUENCE_TYPE=RNA

3.2.2 (Nov 23, 2003)

1. Simulation with more than one probe (N-plex ability)!
2. Automatic BLAST of your pimers/probes WHILE they are being designed!
3. See the position of your primer/probe in your Simulation Results Tab!
4. Enhanced memory management so you can fold longer targets!

Details of these features are as follows:

1. Primer Position on Target Displayed in Sequences Tab
After you design your primers and probes, you may copy these into your experiment. You can now see the start position of the 3’ end of your probe on your target on your Results Summary Tab, after a simulation.

2. Settings Tab

a. N-plex Ability: If you want to see the thermodynamic parameters of multiple probes against one target, check on “Generate N-plex Structures.” The visualization of the N-plex species…coming soon.
b. BLAST Designs: If you want to run an automatic blast for all of the primers which are designed against your target, check on “BLAST Designs” and specify the local FASTA file (.fas) in the BLAST DB box. For example, here are the steps for primer design for a yeast gene.

i. Choose your target gene A – add into Sequences Tab. Under Description, write its accession number.
ii. Specify the solution conditions in the Settings Tab
iii. Download the yeast genome or transcriptome (depending on what you are doing) as a FASTA file.
iv. Settings Tab – Enable BLAST Designs and specify the FASTA file in your directory.
v. Designs Tab – choose your target, specify primer pair and advanced parameters (see additional notes below).
vi. Run Design: VO3 will design primer pairs for your gene (as described in the accession number) while BLASTing against the specified database. This ensures that your primer pair will not pick up something else in the genome. Adding the accession number of your gene into the “Description” box in the Sequences Tab tells OMP not to blast against your gene since then you will have 100% similiarity with the designed primer.

3. Designs Tab

a. Save custom advanced parameters: if you design your own advanced parameters, you can right click and save it under “Save Custom Strategy” for future repeated use.
b. Advanced parameters BLAST designs options

i) MAX BLAST HITS: the maximum number of hits your primer gives against your FASTA database
ii) MAX BLAST MATCH LEN: the maximum nucleotide length on each hit

4. OMP Simulation Engine
With some creative thinking and new memory management, our development team has produced OMP secondary structure simulation memory requirements, bringing you the ability to fold longer targets.

NEW OMP FOLDING MEMORY REQUIREMENTS
nt RAM
10 19 MB
50 19 MB
100 19 MB
500 27 MB
1000 51 MB
1500 91 MB
2000 147 MB
2500 219 MB
3000 307 MB
4000 531 MB
5000 819 MB
10000 3219 MB

3.1.2 (Nov 6, 2003)

1. Sequences Tab: “Fixed probe” now works as a function in a simulation.

2. Sequences Tab: a bug in saving and reloading low concentrations has been fixed. For example, OMP would save 25 pM as 25.000000000000004 pM.

3. Results Summary: the color of the bend points have been changed so they are more apparent in move mode.

4. Sequences Tab affecting Design: updated to use improved RNA-DNA parameters directly in optimization of probes and primers design for RNA targets.

5. Designs Tab: a bug in the amplification window has been fixed. In some designs, the reverse primer was not being included in the window.

6. Designs Results: each primer or probe result now is given a Q-score, the optimal score being 1000.
Q-score = 1000 – sq root(the algorithm score)

Algorithm score = sum of the absolute values of all the deviations from the optimal value (with specified weights) of all the categories in the advanced parameters grid.

Thus, if all of the parameters were optimal, Q-score = 1000 – sq root(0) = 1000.

3.1 (Sept 19, 2003)

1. Automatic OMP update: Goto Help, Check for Program Updates and the software will give you the option to automatically install latest updates

2. Auto tailfolding

a. Goto Settings tab, Advanced Settings Section
b. Tail folding auto threshold default number = 500 (you can change)
c. Input in sequences for targets and probes/primers in Sequences Tab
d. Options for Tailfolding in Sequences tab

i. TRUE: Simulation will always consider tailfolding
ii. FALSE: Tailfolding is off
iii. AUTO: If target sequence is greater than 500 nt, tailfolding will automatically shut off

3. Primer Position on both strands
In Design Results Tab: AS Pos = the position of the primer/probe on the antisense strand of the reported nt in the POS column. For example, forward primer POS = 250, reverse primer As Pos = 300 means these oligos are at nt 250 and 300 on the sense strand.

4. Amplicon Size Reporting
In Design Results Tab: Am Len = size of the amplicon produced by the two primers

5. Sequence Position and Variation Position in Sequence Editor
In the Sequences input box, you can now see which nt position the cursor is at (single or sequential)

6. DNA Display: Click on “View” for secondary structure,

a. The most frequently used functionalities are on top of the window.
b. Right click and select “Load binding sites.” You can see the primers and probes displayed on your target structure.
c. Auto Adjust: your structure will be redrawn so the sequence will not be on top of each other
d. Full zoom will show entire target

7. Improved error checking for viable primer designs.

3.0 (Aug 28, 2003)

1. Increased numbers of input sequences in one experiment to 5000.

2. Ability to Sort and Arrange Experiments under the File Tab.

3. Additional strategies for Design Tab.

a. Fixed 5’: your probe or primer can have a designated, fixed 5’ position on a specified target
b. Fixed 3’: your probe or primer can have a designated, fixed 3’ position on a specified target
c. Enumerate: ability to design tiles of probes against your one target
For example, if you want to find the most optimal probe along a sequence of 1 kb, enter this sequence into the experiment, use it in your designs window and choose “enumerate” as your strategy. Customize the function (ie. same Tm) using the advanced parameter grid, for your needs.

4. New functionalities in Design Advanced Parameters

a. Variation Position: the position of your variation (SNP) within your probe

Points B-f are for oligonucleotide probe pair designs. In designing allele-specific probe pairs for a SNP, you can specify the SNP location within each probe and/or vary the position or length of these two probes. These are specified by the following fields which can be modified to meet your needs.

b. Allele Length Difference: the nucleotide (nt) length difference between the two probes specific to each allele
c. Allele Var Pos Diff: the nt length difference between the variation positions of your two allele-specific probes
d. Allele Start Position Diff: the nt length difference between the two start positions of the two probes
e. Allele Tm Diff: difference between Tm of the probe with the correct target and the probe with the other mismatched allele
f. Allele dG Diff: difference between dG of the probe with the correct target and the probe with the other mismatched allele