|
Upgrades
AlleleID 6.01 Released
AlleleID now offers compatibility with Leopard, Mac OS X 10.5. The upgrade also accommodates the latest changes at the mFold and the NCBI BLAST server including support for the latest genomic database.
AlleleID 6.00 Released
AlleleID can now design MLPA probes compatible with PamChip® microarrays of PamGene. MLPA users have the choice of either designing mRNA specific, DNA specific or mutation specific probes based on research needs thus reducing the detection time.
AlleleID 5.01 Released
NCBI recently redesigned the BLAST pages, changing the default interface. The support for old pages was removed on June 11, 2007 and a few more databases were added. AlleleID 5.01 is released to accomodate these changes.
AlleleID 5.00 Released
MLPA® Assays- With AlleleID 5.00, you can design highly specific probes for MLPA® assays. MLPA, short for Multiplex ligation-dependent probe amplification is popularly used for detection of amplifications and deletions in a variety of genes. Using AlleleID you can design MLPA® probes, both for copy number detection and mutation studies.
Use Pre-designed Probes- For published or pre-designed probes, AlleleID now designs compatible primers and completes your species or taxa specific assays.
Design Degenerate Primers- You can even design degenerate or mismatch tolerant primers for taxa assays where conservancy is disturbed due to presence of mismatches.
Multiplex TaqMan® Assays- AlleleID now includes comprehensive support for multiplexing. The program is now equipped with innovative proprietary algorithms to design the most optimal primer-probe sets for multiplex reactions. The sets are chosen by minimizing Tm mismatches and cross dimerization and are made available in a sortable list. For multiplex assays, you can even design oligos for additional sequences that are compatible with the pre-designed sets for certain sequences. This feature may be most useful for incorporating a well-proven reference or housekeeping gene in a reaction. It is also possible to check the suitability of pre-designed primer sets for a multiplex reaction.
Batch BLAST and Template Structure Search- You can now perform BLAST and template structure search for multiple sequences in a single search run.
AlleleID
4.02 Released
The upgrade accommodates the changes at the NCBI BLAST server
and includes fixes to reported problems.
AlleleID 4.01 Released
The upgrade accommodates the changes at the NCBI BLAST server.
AlleleID 4.00 Released
Splice Variant Microarrays- With AlleleID
4, you can now design microarrays to detect splice variants.
To detect alternative splicing events, AlleleID designs two
types of probes called junction probes and intra-exon probes.
Junction probes span exon-exon boundaries while intra-exon
probes lie entirely within a single exon, making AlleleID
an effective tool in designing experiments to test novel splice
forms.
SYBR® Green and TaqMan® MGB oligos for Species/Taxa
Specific Assays- Design support is also available
for species identification and taxa discrimination assays
using SYBR® Green primers and TaqMan® MGB assays.
The primers designed in the SYBR® Green mode can be used
to design compatible oligos. Design a species specific or
taxa specific assay in the SYBR® Green design mode. When
ready to design the probes, check the option: “Use Primers
Designed In the SYBR Green Mode” in the TaqMan®
or beacon design mode. AlleleID imports the primers for each
sequence in the alignment and designs compatible probes.
Includes support for the latest genomic databases available
at NCBI.
AlleleID 3.01 Released
Includes support for the latest genomic databases available
at NCBI.
AlleleID 3.00 Released
AlleleID now includes support for the following:
Use Pre-designed Primers- For a partial set
of pre-designed or published primers, AlleleID can design
compatible primers for the rest of the sequences for species
or taxa specific assays. You can load a pre-designed primer
set or associate a library of primers and then ask AlleleID
to design compatible probes as well.
TaqMan® MGB probe design- In addition
to standard TaqMan® probes, TaqMan® Minor Groove Binding
(MGB) probes can now be designed. Using an MGB moiety allows
the use of shorter probes, improving discrimination, and providing
greater flexibility in probe design.
"Minimal Set" for Taxa Discrimination- If
the homology between the aligned sequences is low and it is
not possible to design assays with a single probe for each
Taxa even after tolerating mismatches, the Minimal set option
within AlleleID can be used. When chosen, AlleleID designs
the minimal number of probes required to identify each taxa.
This feature is an important option for studies involving
phylogenic relationships among sequence groups which have
two or more highly conserved subgroups, for example, the same
taxa evolved in two or more different geographical locations.
Desktop BLAST- BLAST search sequences against
local custom databases without the need of setting up a server
on a separate machine. Simply save the sequence files (.txt
or .fa) on your computer and ask AlleleID to BLAST search
your query sequence against them.
Genomic Databases Support- All, including
the latest genomic database additions at NCBI, are now accessible
through the program.
AlleleID 2.01 Released
Includes support for the latest genomic databases
available at NCBI.
AlleleID 2.00 Released
Species Specific Microarrays- To design probes
for species identification, the program aligns the sequences
using ClustalW algorithm. It then analyzes conserved and species
specific regions to design probes to identify the species
of interest from the mix.
Cross Species Microarrays- AlleleID can
design cross species arrays for related organisms. This feature
is generally used when a genome draft for the organism of
interest is not available. AlleleID analyzes the conserved
regions of related organisms to design probes that are likely
to work for the organisms or species of interest. You could
thus use, say zebra fish arrays, to detect expression of telapia
genes. Such chips can also be used in assessing the effects
of contaminants.
Microarray Probe Design for Gene Expression and SNP
Genotyping- Version 2.00 of AlleleID includes a separate
module for supporting high throughput microarray probe design.
You will now be able to design thousands of efficient, highly
specific oligos to make microarrays for SNP genotyping and
expression studies with the click of a button. The probes
designed will be free of secondary structures and with uniform
Tm values ensuring a high rate of success of microarray experiments.
New in AlleleID 1.01
AlleleID connects to the NCBI server to BLAST search
your sequences and automatically interpret the results to
design specific primers.
NCBI's BLAST server underwent a few changes over the last
few days. One of the most significant being the availability
of a new version of the BLAST formatter. To accommodate these
changes we have released an upgrade. With this upgrade you
will now be able to BLAST search your sequences seamlessly.
Array Designer 4.25 Released
The upgrade includes fixes to reported problems.
Array Designer 4.24 Released
NCBI recently redesigned the BLAST pages, changing the default interface. The support for old pages was removed on June 11, 2007 and a few more databases were added. Array Designer 4.24 is released to accomodate these changes.
Array Designer 4.23 Released
The upgrade accommodates the changes at the NCBI BLAST server.
Array Designer 4.22 Released
The upgrade accommodates the changes at the NCBI BLAST server.
Array Designer 4.21 Released
Includes support for the latest genomic databases available
at NCBI.
Array Designer 4.20 Released
Design Tiling probes: Version 4.20 of Array
Designer designs evenly tiled probes that are tiled across
the genome which facilitates genome wide analyzes of many
important biological functions including site of chromatin
modification and sites of DNA methylation.
The new version also designs overlapping probes tiled across
genome to cover an entire genomic region of interest facilitating
genome wide analysis.
Array Designer 4.12 Released
Includes support for the latest genomic databases available
at NCBI.
Array Designer 4.11 Released
With Array Designer 4.11, you can select an E-value
for avoiding homologies and manage your projects better.
Array Designer 4.10 Released
We are pleased to announce version 4.10 of Array Designer
which includes the following:
Resequencing Array Design- In addition to
standard probes, you can now design resequencing arrays. With
custom resequencing arrays, you can detect SNP and other sequence
variations in a large number of samples for applications such
as biowarfare pathogen studies, predisposition and resistance
to disease or discovering the genetic basis of phenotypic
traits.
The challenge in designing arrays for resequencing by hybridization
is to achieve the lowest possible false positive rate. With
version 4.10 simply connect to the popular Repeat Masker using
the handy link and Array Designer will avoid creating spots
that may generate false positives.
Project BLAST- One of the vexing problems
in resequencing array design is false base calls caused by
inter-template cross hybridization. Array Designer offers
an innovative and unique Project BLAST capability
to identify these regions and recommends a multi-chip solution.
With this special BLAST function, you can BLAST search all
the sequences in the project against each other. With the
homologies observed, you can choose which sequence or sections
of a sequence can be arrayed on the same chip. As observed,
highly homologous sequences lead to cross hybridization and
compromised data quality. This feature is very useful if you
have to array more than one sequence on a single chip.
Desktop BLAST- You can now BLAST search sequences
against local custom databases without the need of setting
up a server on a separate machine. Simply save the sequence
files (.txt or .fa) on your computer and ask Array Designer
to BLAST search your query sequence against them.
Array Designer 4.01 Released
Array Designer connects to the NCBI server to BLAST search
your sequences and automatically interpret the results to
design specific primers.
NCBI's BLAST server underwent a few changes over the last
few days. One of the most significant being the availability
of a new version of the BLAST formatter. To accommodate these
changes we have released an upgrade. With this upgrade you
will now be able to BLAST search your sequences seamlessly.
New in Array Designer 4.00
Whole Genome Array Design- With Array Designer
you can study entire organisms effortlessly, characterizing
transcriptomes, discovering differentially and alternatively
spliced transcripts, DNA sequence variation in individuals
or populations, and comparative genome hybridization (CGH).
Design Tiling primers- design tiling primers
for small to medium sized genome that helps identify the DNA
binding protein targets, methylome analysis, characterization
of transcriptome.
New in Array Designer 3.00 and later:
1. The Human, Rat and Mouse genome databases on the BLAST
server were reorganized by NCBI. The databases were further
classified into genome (all assemblies) and genome (reference
only). To accommodate these changes we released the upgrade.
2. Automatic interpretation of BLAST results to design highly
specific PCR primers.
3 . Ability to BLAST search oligos and templates against
all the nucleotide redundant databases available at NCBI
to verify the specificity of design.
4 . Comprehensive support for long probe design.
5 . Includes support for the latest genomic databases available
at NCBI.
6 . Ability to load sequences directly from dbSNP.
7 . A Mac and Linux version is also available.
8 . Simplified web based activation scheme (Array Designer
customers, please click
here for details)
|
 |
Beacon Designer 7.20 Released
Beacon Designer now provides suitable control primers and probes for MethyLight assays by designing them for unmethylated and untreated DNA sequences. Amongst a host of other improvements, Beacon Designer now graphically displays the regions of homology and secondary structures and where the designed oligos are located with respect to these. To adjust the similarity threshold according to the type of technology or your own stringency criterion, Beacon Designer now enables you to set either the e value, the identity or both. Based upon the values chosen, the hits reported will be avoided during oligo design.
Support for all the genomic databases available at NCBI is also included.
Beacon Designer 7.03 Released
The upgrade accomodates the latest changes for folding templates at the mfold server.
Beacon Designer 7.02 Released
The upgrade includes fixes to reported problems.
Beacon Designer 7.01 Released
NCBI recently redesigned the BLAST pages, changing the default interface. The support for old pages was removed on June 11, 2007 and a few more databases were added. Beacon Designer is released to accomodate these changes. It also includes fixes to problems reported.
Beacon Designer 7.00 Released
Scorpions® Assays- Using Beacon
Designer 7.00, you can now design scorpions® primers and
probes. Scorpions® represent the most recent development
in real-time PCR chemistry since this technology is not dependent
on enzymatic cleavage of the probe. The stem-loop format is
a common approach for specific detection of PCR products in
which the probe element and primer element are physically
coupled during the reaction. It is ideally suited for many
applications that require rapid detection such as viral load
testing and RNA profiling.
With Beacon Designer you can not only design scorpions®
primers and probes with a click of a button but also use pre-designed/published
primer sets and design compatible oligos. The scorpions®
primers are screened for all possible secondary structures
and scorpions® probes are checked for alternate structures.
Batch BLAST- You can now BLAST search multiple
sequences.
All databases available at NCBI are now accessible through
the program.
Beacon Designer 6.01 Released
The upgrade accommodates the changes at the NCBI BLAST server.
Beacon Designer 6.00 Patch Released
Includes fixes to the reported problems.
Beacon Designer 6.00 Released
MethyLight TaqMan® Assays- With Beacon
Designer 6.00, you can design TaqMan® oligos for MethyLight
assays. MethyLight assay is widely used for measuring DNA
methylation levels and has been proved to be an efficient
and highly sensitive technology. Beacon Designer designs quantitative
Methylight assays which utilizes fluorescence-based real-time
PCR (TaqMan®) technology for detecting methylated DNA.
A short note on DNA
Methylation
Improved Sequence View- Included, in addition,
is the ability to copy and paste sequences from the Sequence
View. Beacon Designer displays the primers and probes on the
sequence in the right pane. You can now copy and paste the
primer, probe or entire sequence at the right click of the
mouse.
All databases available at NCBI are now accessible through
the program.
Beacon Designer 5.11 Released
Includes support for the latest genomic databases available
at NCBI.
Beacon Designer 5.10 Released
Multiplex TaqMan® Assays- Beacon Designer
5.10 now includes comprehensive support for multiplexing.
The program is now equipped with innovative proprietary algorithms
to design the most optimal primer-probe sets for multiplex
reactions. The sets are chosen by minimizing Tm mismatches
and cross dimerization and are made available in a sortable
list. For multiplex assays, you can even design oligos for
additional sequences that are compatible with the pre-designed
sets for certain sequences. This feature may be most useful
for incorporating a well-proven reference or housekeeping
gene in a reaction. It is also possible to check the suitability
of pre-designed primer sets for a multiplex reaction.
The latest genomic databases available at NCBI are also supported.
Beacon Designer 5.01 Released
Beacon Designer connects to the NCBI server to BLAST
search your sequences and automatically interpret the results
to design specific primers. Version 5.01 includes support
for the latest genomic databases available at NCBI.
New in Version 5.00 of Beacon Designer
We are pleased to release version 5.00 of Beacon Designer
which includes:
LNA™ Probe Design-In addition to standard
TaqMan® probes, the increasingly popular LNA™ or
Locked Nucleic Acid™ substituted TaqMan® probes
can now be designed. Incorporation of the LNA™ bases
significantly increases thermal stability, making shorter
probes possible for standard reaction conditions. Furthermore,
it improves hybridization specificity and enhances gene quantification
and alleleic discrimination accuracy.
NASBA Beacon Design- Beacon Designer also
helps you design molecular beacons for both standard as well
as NASBA assays for single template, multiplex or alleleic
discrimination. NASBA, short for Nucleic Acid Sequence Based
Amplification, is gaining acceptance as a single-step isothermal
RNA-specific amplification process. It amplifies mRNA
in double-stranded DNA background without temperature cycling.
Settable Parameters for Mfold- You can now
alter the temperature, Mg++ ion and monovalent ion (Na+) concentration
in Beacon Designer for folding templates at the Mfold server.
Genomic Databases Support- Includes support
for the latest databases available at NCBI for BLAST search.
Beacon Designer 4.02 Released
Beacon Designer connects to the NCBI server to BLAST search
your sequences and automatically interpret the results to
design specific primers.
NCBI's BLAST server underwent a few changes over the last
few days. One of the most significant being the availability
of a new version of the BLAST formatter. To accommodate these
changes we have released an upgrade. With this upgrade you
will now be able to BLAST search your sequences seamlessly.
New in Beacon Designer 4.01
Beacon Designer connects to the highly accurate Mfold server
to fold templates and calculate the beacon Tm. The Mfold server
underwent a few changes over the last couple of days. To accommodate
these changes we have released an upgrade. With this upgrade
you will now be able to fold templates and design molecular
beacons.
New in Beacon Designer 4.00
- SYBR Green primer design mode- design
primers for SYBR Green assays. If you choose, these primers
can be exported to the TaqMan®, FRET or molecular beacon
design modes to design compatible dual labeled probes.
- FRET probe design mode- design optimal
FRET probes and compatible primers using this module. A
list of alternate primer and probes is made available for
you to choose the most appropriate set for your needs. You
will also be able to evaluate pre-designed primers and probes.
- Ability to generate an attractive report of the
designed assays- You will now be able to create
an attractively formatted report for the assays you designed.
It should be helpful in record keeping and for sharing information
with colleagues. The report helps visualize the positions
of the primers and probes on the sequence, includes a list
of the alternate primers and probes, displays primers, probe,
amplicon and sequence properties and the design parameters
used.
- Includes support for the latest databases available at
NCBI for BLAST search and fixes to reported problems.
New in Beacon Designer 3.00 and
later
The Human, Rat and Mouse genome databases on the
BLAST server were reorganized by NCBI. The databases were
further classified into genome (all assemblies) and genome
(reference only). To accommodate these changes we released
the upgrade.
Ability to BLAST search oligos and templates against all
the nucleotide redundant databases available at NCBI to verify
the specificity of design.
- Facility to BLAST search probes for specificity of design.
- Includes support for the latest genomic databases available
at NCBI.
- Includes the changes at the Mfold server.
- Simplified web based activation scheme (Beacon Designer
customers, please click
here for details.
PrimerPlex 1.01 Released
PrimerPlex now offers compatibility with Leopard, Mac OS X 10.5. The upgrade also accommodates the latest changes at the NCBI BLAST server including support for the latest genomic database.
SimGlycan version
2.51 Released
New in this version:
SimGlycan now also analyzes glycopeptides in addition to released glycans. You can quickly resolve the structure of a glycan in a glycopeptide molecule by specifying the sequence or mass of the attached peptide moiety.
The new version also supports 20 more monosaccharides, over the existing 42.
SimGlycan version
2.50 Released
New in this version:
You can now generate scatter and column plots, specify an m/z range to display specific plot sections and export plots for sharing results with your colleagues or for publication purposes.
SimGlycan now enables you to search for glycans with chemical derivatives used for reducing end modifications even if the derivative is not available in the program's database. For example, say you are working with 2AB (2-aminobenzamide) labeled glycans and SimGlycan does not have it listed as a derivative, simply enter the mass. SimGlycan would analyze all possible combinations in the database and display a list of the most closely matched glycans in a ranked order.
You can now load MS/MS data in standard mzXML and mzData file formats. Using third party tools, the data from any mass spectrometer can be converted to mzData and mzXML, enabling SimGlycan to seamlessly integrate with your mass spectrometer output.
SimGlycan now also supports MS/MS data generated on multi-charged ions.
SimGlycan version
2.21 Released
New in this version:
The upgrade includes improved data handling capabilities for SimGlycan. Users can now expect better and faster search results using the product's new improved search algorithm.
SimGlycan version
2.20 Released
New in this version:
The upgrade includes the ability to search for glycans based on their ID, sequence, composition or mass. SimGlycan displays the glycan structure, fragments, mass, class, reaction and pathway.
In addition, you can rename the Glycan ID and the MS profile to a name of your choice amongst a host of other improvements to give you better and faster results.
SimGlycan version
2.10 Released
New in this version:
With SimGlycan 2.10, you will be able to select the proposed structures of interest manually. The program highlights the experimental m/z values that match those of theoretical fragments for easy selection and then generates an instant annotated stick spectrum or MS profile of them. It also enables you to assign your own rank to predicted structures, add comments and search fragments by their mass, name and m/z values.
SimGlycan version
2.00 Released
New in this version:
The upgrade includes support for sodium as an adduct and
support for 16 more monosaccharides, over the existing 26.
SimGlycan version 1.50 Released
New in this version:
Export Results- With SimGlycan 1.50, you
can export glycan search results and generate an attractively
formatted report for viewing or printing.
Text File Input- Supports text file format
for loading MS/MS data in addition to excel files.
Manual MS/MS Data Input- You can manually
type-in or copy/paste the MS/MS data into SimGlycan.
Database Updates- Supports additional monosaccharides.
SimVector version 4.22 released
The upgrade includes fixes to reported problems.
SimVector version 4.20 released
New in this version:
Mutagenic Primer Design- SimVector 4.20
includes a site directed mutagenesis primer design module
called MutaPrimer. It designs primers for QuikChange QuikChange
XL, Stratagene's site directed mutagenesis kit. The kit supports
point mutations, insertions and deletions.
MutaPrimer designs mutagenic primers that fully comply with
the primer design guidelines published by Stratagene for QuikChange.
According to the guidelines, the most important parameters
are Tm and lengths required for the flanking regions. You
can start the primer search for either the DNA sequence or
the amino acid sequence with just a click of a button.
SimVector version 4.10 released
New in this version:
- Database Architecture: SimVector ported
to a database architecture with improved sequence handling
& analysis capabilities.
- Increased Sequence Limits: Import longer
sequences, upto 2.5 MB.
SimVector version 4.01 released
SimVector 4.01 includes fixes to reported problems.
SimVector version 4.00 released
New in this version:
- Multiple Cloning Site (MCS) Display-
Commercial companies generally display MCS's in a unique
format, with enzymes one above the other in a vertical list.
Version 4.00 of SimVector identifies the MCS's by interpreting
GenBank header annotations when available, or you can specify
them manually. It even has the smarts to list only the enzymes
that cut within the MCS and nowhere else. This special format
we call the Bracket View.
- Multiple Fonts- The program can now display
any enzyme or feature name using multiple fonts. It is common
to list an enzyme thus: Hind III, where the bacterium
of origin is listed in italics, but not the number. Coupled
with the MCS bracket view, SimVector now has all the functionality
to draw plasmids and export them in several vector graphic
or bitmap formats.
- ORF Search- Version 4.00 now includes
the search capability to find ORFs in the chosen reading
frames, identified with the selected start and stop codons,
and compliant to the specified minimum length. With a click
of a button, you can now ensure that the construct remains
in-frame after cloning. The graphical ORF display is always
ready for reference and further analysis.
- Sequence Translation- With version 4.00
you can translate sequences for simulating expressed proteins
and to check for possible reading frame errors.
SimVector version 3.00 released
New in this version:
1. Undo/Redo capability
2. Curved text support for feature names
3. Automatic feature overlap avoidance so that no feature
remains "hidden"
4. Copy/paste functionality that carries feature annotations
along with the sequence
5. Simplified web based activation scheme (SimVector customers,
please click
here for details)
TMA Foresight 3.01 Released
The upgrade includes fixes to reported problems.
TMA Foresight 3.00 Released
TMA Foresight now supports the following:
Removing Multicollinearity from Data:
Multicollinearity in a dataset is observed due to a strong correlation between independent variables. It obscures the statistical significance of such variables, leading to incorrect conclusions about the relationships between independent and dependent variables. This could be particularly problematic when you would like to study the contribution of an individual variable.
With this version, you can eliminate the effect of multicollinearity from your data at the click of a button.
Partial Correlation for Multiple Controlling Variables:
Partial correlation is used to study the relationship between two variables while controlling the effects of the third. This upgrade enables you to study the correlation between two variable by controlling the effect of more than one variable at a time.
Also includes general improvements and fixes to the reported problems.
TMA Foresight 2.50 Released
TMA Foresight is now equipped to analyze biomarker expression data in addition to performing survival analysis. You can now perform analysis such as clustering and correlation without providing survival data. You should be able to apply all the statistical techniques included directly to immunohistochemical data to identify diagnostic biomarkers, cluster them and draw inferences from other known markers. When used in conjunction with expression profiling, TMA Foresight is now a more powerful tool for evaluating and interpreting TMA data.
TMA Foresight 2.02 Released
The upgrade includes fixes to reported problems.
TMA Foresight 2.00 Released
- Data Filtering- With TMA Foresight 2.0,
filter the tissue microarray data using logical operators.
- Correlation Analysis- Explore linear,
monotonic, curvilinear, non-linear relationships between
two covariates. Various correlation coefficients, viz.,
Phi, Cramer's V for nominal, Spearman's rank correlation,
Kendall's tau-b and tau-c for ordinal and Pearson's coefficient
for ratio scale, can be used for the analysis. For analyzing
correlation between any two variables by negating the influence
of other variables, run a partial analysis.
- Principle Component Analysis- TMA Foresight
helps you quickly generate clusters from 2D scatter plots
generated from a principal component analysis using its
point-and-click functionality. The Kaplan Meier plot and
results of the Log Rank test are updated accordingly.
- Test of Independence- TMA Foresight
helps you study the likelihood of any two categorical variables
being associated using Fisher's Exact and Chi-square tests.
|
 |
Xpression Primer 3.03 Released
Includes fixes to the reported problems.
Xpression Primer 3.02 Released
Includes support for the latest genomic databases available
at NCBI.
Xpression Primer 3.01 Released
Xpression connects to the NCBI server to BLAST search your
sequences and automatically interpret the results to design
specific primers.
NCBI's BLAST server underwent a few changes over the last
few days. One of the most significant being the availability
of a new version of the BLAST formatter. To accommodate these
changes we have released an upgrade. With this upgrade you
will now be able to BLAST search your sequences seamlessly.
New in Xpression Primer 3.00 and later:
1. Includes support for the latest genomic databases available
at NCBI
2. Simplified web based activation scheme (Xpression Primer
customers, please click
here for details)
|
