Life Science Software

Showing posts with label Probe designing Software. Show all posts

Expression Primer - Primer Cloning designing Software

A revolutionary tagged primer design tool for designing expression cloning experiments

Extensive Assay Support for Tagged Primer design
Use the sophisticated algorithm of Xpression Primer to design thousands of tagged primers for expression cloning systems such as Gateway®, BD In-Fusion™, epitope and TOPO® Tools. You can choose to amplify an entire ORF or generate N terminal or C terminal fusion proteins. Xpression Primer ensures that the reading frame of the amplified ORF is conserved. To work with other expression systems, simply add functional tags of your choice and design tagged primers.

Successful Amplification with Nested PCR
To ensure the success of your PCR experiment, let Xpression Primer design nested tagged primers to amplify ORFs. You can locate the outer primers anywhere in the UTRs or in regions of no significant homology. Xpression Primer will BLAST your sequences, automatically interpret the results and design highly specific primers. The tagged inner primer pair amplifies the PCR product generated by the outer pair with little or no non-coding regions. You can also choose from a list of alternate primers to better meet specific experimental needs.

Sequencing for Product Verification Made Easy
The versatile algorithm of Xpression Primer can design optimal sequencing primers for multiple sequences in a single run. It picks forward primers across the amplicon at a specified interval and reverse primers staggered on the opposite strand. You can export the results for several popular well plate configurations.

Generate Precise Transcripts
Design primers to generate sense or antisense transcripts for in vitro expression studies.

Web Savvy
Xpression Primer searches Entrez and downloads batches of ORF sequences directly into the program.

Software Link : Expression Primer - Primer Cloning designing Software

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Oligo Design for Multiplex PCR & High Throughput SNP Genotyping and Analysis

PrimerPlex is an efficient and sophisticated tool for designing oligos for multiplex assays. Multiplex assays facilitate amplification of multiple targets in a single reaction vessel, reducing both the time and cost of experimentation.

PrimerPlex designs oligos for multiplex PCR assays and for suspension array based systems such as Luminex 100, Luminex 200 and Bio-Plex 200. Such systems offer a versatile platform for multiplexed nucleic acid detection in a 96-well format. PrimerPlex designs specific capture probes for direct hybridization assays and primers for Allele Specific PCR Extension (ASPE) assays.

The multiplex assays are used for gene expression analysis (end point detection using gel electrophoresis) and for high throughput SNP applications such as genotyping, pathogen detection, strain typing, and haplotyping. To ensure specificity, the oligos are designed after avoiding the regions of homologies identified by a BLAST search. PrimerPlex then checks the oligos for cross reactivity and minimizes Tm mismatches to give you the best possible multiplex set. In the process, it analyzes millions of possible multiplex primer sets in a few seconds and presents a list of alternate sets to you as well.

Design Options

Multiplex PCR Primer Design
PrimerPlex designs standard primers for a 30-plex multiplex PCR assay. It uses proprietary algorithms to design optimal primer sets under uniform reaction conditions for up to 30 targets. Primer sets are identified after screening all the primers in a pool and minimizing Tm mismatches. All the multiplex primer sets are analyzed for cross hybridization to ensure specific amplification and high signal strength.

Direct Hybridization Assays

PrimerPlex designs optimal allele specific capture probes for high throughput SNP genotyping assays. The probes are designed such that the mutations are at their centers to maximize differentiation. Each one of the probes designed is checked for its suitability in a multiplex reaction. For amplifying the templates, the program designs SNP flanking primers as well. This functionality makes PrimerPlex the only software product capable of designing probes for 100 individual targets for a multiplex assay.

ASPE Assays

Another approach to detect mutations is to use a solution-based sequence specific enzymatic reaction such as Allele Specific Primer Extension (ASPE) to determine the target genotype. PrimerPlex designs highly specific primers for multiplexed ASPE assays. The ASPE primers are designed such that the mutations lies at their 3' end. PrimerPlex also designs primers to amplify the target sequence for ASPE assays.

Software Link : PrimerPlex - PCR Oligo designing Software

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Automate your real time PCR primer and probe design
Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.

Specific and Efficient Design: How Beacon Designer™ Makes it Possible?

You can BLAST search sequences and search for template structures from within the program. The results of both these searches are used while designing primers and probes. The regions that exhibit significant cross homologies and template structures are avoided automatically during the design.

Design Options Available

SYBR® Green Assay Design
SYBR® Green is perhaps the most commonly used real time PCR chemistry. Beacon Designer™ designs
SYBR® Green PCR primers and helps you evaluate pre-designed SYBR® Green PCR primer sets.

You have complete control over the design parameters or you can use the default values, chosen after considerable research and communication with experts.

HRMA Assay Design
Beacon Designer™ offers a comprehensive solution for mutation detection. High Resolution Melting Analysis (HRMA) is a more cost-effective method than probe-based genotyping analysis. The program employs proprietary algorithms that enables designing the best primers for detecting mutations.

High Resolution Melting Analysis primers are designed flanking a mutation of interest to generate the shortest possible amplicons with detectable melting temperature variation. The primers are designed avoiding template secondary structures, assuring efficient primer extension. The HRMA primers designed can be BLAST searched against nucleotide databases at NCBI to check their specificity. Pre-designed or published primers can also be analyzed.

Dual Labeled Probe Design
Beacon Designer™ currently supports four probe based chemistries:

TaqMan® Probes
Use Beacon Designer™ for optimal TaqMan® probes that help you study the differential gene expression or study SNP (single nucleotide polymorphisms) using TaqMan® SNP genotyping assays. You can also choose to design the increasingly popular Locked Nucleic Acid (LNA™) substituted TaqMan® probes, which are more stable than standard TaqMan® probes. To study DNA methylation, Beacon Designer™ helps design primers and TaqMan® probes for MethyLight assays. MethyLight is a high throughput assay used to discriminate between methylated and unmethylated DNA. Using Beacon Designer™, you can design suitable control primers and probes by designing oligos for the methylated and the unmethylated strands, and for the untreated DNA sequence. With any of these chemistries, you could evaluate a pre-designed/published primers or TaqMan® probes. The design results are reported in a ranked order, giving you a list of alternates to choose from. Depending on the oligo properties, a rating is assigned. Please read the Rating section in the online help for details.

Molecular Beacons
Design or evaluate standard molecular beacons or molecular beacons for NASBA® assays. NASBA® is a primer-dependent technology that can be used for the continuous amplification of nucleic acids in a single mixture at one temperature. You can now design molecular beacons for NASBA® assays for single template or multiplex reactions.

Scorpions®
Beacon Designer™ supports the design of Scorpions® primers and probes. Scorpions® assays are important in that they are independent of the enzymatic cleavage of the probe. The primer and probe element are physically coupled during the reaction. Read more about the Scorpions® technology.

FRET Probes
Beacon Designer™ supports design and evaluation of pre-designed FRET probes. FRET probes that are compatible with pre-designed SYBR® Green primers can be designed in Beacon Designer™.
Multiplex Real Time PCR Assays

With Beacon Designer™ you can design TaqMan® based multiplex real time PCR assays for upto five sequences including reference gene selection.

Software Link : Beacon Designer - PCR Primer designing Software