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AlleleID is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification
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AlleleID®

Upgrades

AlleleID® 7.81 Released


The upgrades accommodates latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems.

The version is now compatible with Mavericks, Mac OS X 10.9.

AlleleID® 7.80 Released

The upgrade accommodates the latest genomic databases available at the NCBI BLAST server and fixes to reported problems. The version is now compatible with Windows 8.

AlleleID® 7.75 Released

The latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems are also accommodated.

AlleleID® 7.74 Released

The latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems are also accommodated.

The upgrade offers compatibility with Windows 64bit OS.

AlleleID® 7.73 Released

The upgrade offers compatibility with Lion, Mac OS X 10.7.

The latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems are also accommodated.

AlleleID® 7.72 Released

The upgrade includes fixes to reported problems.

AlleleID® 7.71 Released

The version includes improvements in Taxa Specific primer-probe design algorithm and fixes to reported problems.

AlleleID® 7.70 Released

Includes support for the latest genomic databases available at NCBI.

AlleleID® 7.60 Released

The upgrade offers compatibility with Snow Leopard, Mac OS X 10.6. It also accommodates changes at NCBI BLAST server & fixes to reported problems.

AlleleID® 7.50 Released

AlleleID® can now design strain differentiation multiplex assays for Suspension Array systems based on Luminex's xMAP® technology. If you are working with closely related organisms, this functionality will enable you to run experiments in a single reaction vessel.

Support for single template xMAP® assays is also included wherein oligos are designed for rapid and high-throughput detection of nucleic acid sequences. You can even use pre-designed proven oligos and design oligos for the rest of the sequences to form a multiplex set compatible with them.

Additionally, you can use a pre-designed or published or well proven forward or reverse primer and have AlleleID® design the rest of the assay. For example, for a given forward primer, AlleleID® would design the reverse primer for SYBR® Green assays and would design both the reverse primer and the TaqMan® probe for TaqMan® assays.

The multiplexing and design algorithms are enhanced considerably. AlleleID can now design 5-plex assays which are efficient and error free.

The latest genomic databases available at the NCBI BLAST server are also supported.

AlleleID® 7.01 Released

The upgrade includes enhanced support for MLPA probe design based on the new design guidelines laid down by MRC-Holland, the inventors of the technology. The program has been thoroughly tested by MRC-Holland for the accuracy and relevancy of the results. AlleleID can now load sequences from UCSC Genome browser and automatically retrieve exon, repeats and SNP information for further analysis.

The automatic homology avoidance algorithm has been improved considerably to improve the selection of the regions of homology. This and several other parameters have been improvised to enable you to design assays of greater specificity and efficiency.

AlleleID® 7.00 Released

AlleleID® can now design highly specific probes for NEAT assays. NEAT, Non-Enzymatic Amplification Technology, is a genomic testing platform. Using AlleleID® you can design NEAT probes, both for copy number detection and mutation studies.

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 accommodate 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.

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