Search
Browse Categories

AlleleID® Microarray Software


Price: $7,916.00
Item Number: ALID
Arrayit Corporation and Premier Biosoft collaborated to create AlleleID® oligonucleotide design software as the market's most advanced comprehensive solution for probe and primer design for microarray applications including gene expression, single nucleotide polymorphism (SNP) analysis, genotyping, whole genome analysis, tiling, re-sequencing, and many other applications in DNA and RNA microarrays. AlleleID® Microarray Software is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification. With ClustalW multiple sequence alignment at its core, AlleleID® can be used to design species identification/cross species probes for microarrays or real time PCR including SYBR® Green, TaqMan® MGB, TaqMan® probes, Molecular Beacons and real time PCR primers. AlleleID® also offers support for designing microarray experiments for detecting alternative splicing events.

Microarray Software - AlleleID Software to Design Oligonucleotides for Genotyping, Gene Expression, Re-Sequencing, CGH, and PCR Microarrays

AlleleID
Arrayit Corporation and Premier Biosoft collaborated to create AlleleID® oligonucleotide design software as the market's most advanced comprehensive solution for probe and primer design for microarray applications including gene expression, single nucleotide polymorphism (SNP) analysis, genotyping, whole genome analysis, tiling, re-sequencing, and many other applications in DNA and RNA microarrays. AlleleID® Microarray Software is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification. With ClustalW multiple sequence alignment at its core, AlleleID® can be used to design species identification/cross species probes for microarrays or real time PCR including SYBR® Green, TaqMan® MGB, TaqMan® probes, Molecular Beacons and real time PCR primers. AlleleID® also offers support for designing microarray experiments for detecting alternative splicing events. . AlleleID software is fully compatible with Arrayit’s high-speed bioblue bioinformatics computers and highly recommended for VIP™ genotyping customers. Each software purchase includes Arrayit technical support for microarray applications.

Table of Contents

  • Introduction
  • Quality Control
  • Software Overview
  • Software Description
  • Product Contents
  • Software Applications
  • Software Features
  • Computer Requirements
  • Software Screenshots
  • Customer Feedback
  • Technical Assistance
  • Recommended Products
  • Scientific Publications
  • Ordering Information
  • Warranty

Introduction
Arrayit and Premier Biosoft AlleleID® Software improves the precision, speed and affordability of microarray experimentation in research, pharmaceutical development, diagnostics, agriculture, and other areas of life sciences and health care by facilitating both manual and automated design of primers, probes and other types of oligonucleotides. This handbook contains all the information required to take full advantage of AlleleID®, the market’s most advanced oligonucleotide design software.

Quality Control
Arrayit and Premier Biosoft employ the highest quality control (QC) and quality assurance (QA) measures to ensure the quality of the algorithms used in AlleleID®. The finest scientific research was used to develop this software product. When used on conjunction with Arrayit BioBlue computers, AlleleID® is guaranteed to outperform the highest industry standards for oligonucleotide design software tools.

Software Overview
AlleleID® is an oligonucleotide and cDNA microarray design software package that empowers scientists to design thousands of primers and probes for DNA microarray applications in seconds.  It designs probes for SNP detection, microarray gene expression and gene expression profiling. In addition, comprehensive support for tiling microarrays and re-sequencing microarrays is available.

Software Description
AlleleID® is the industry’s most advanced software solution for oligonucleotide design. Customers will appreciate the following features of this software package:

  • Based on the most advanced microarray technology and computer science
  • Complete Arrayit technical support for all microarray applications
  • Manual and fully automated oligonucleotide design
  • Design thousands of oligos in seconds
  • Gene expression, genotyping, tiling, re-sequencing and whole genome applications
  • Upload any sequence locally or globally via the Internet
  • Design sequences to entire genomes effortlessly
  • Optimizes sequences to avoid secondary structure
  • Calculates melting temperatures and hairpin energies automatically
  • Fully compatible with Arrayit microarrays and products from other vendors
  • Optimized for high-speed analysis using Arrayit BioBlue Computing Platforms
  • Remove the guesswork from oligonucleotide design

Product Contents

  • AlleleID® Software CD
  • Product Registration Number
  • Product Registration Sheet

Software Applications
1. BLAST Searches.  AlleleID® designs highly specific oligonucleotides by interpreting the results of a BLAST search performed against any genomic database available at NCBI or a local custom database.  All significant homologies identified are automatically avoided during the oligonucleotide design process.  Repeat regions are identified and automatically avoided as well.

2. Standard Microarray Design.  You can design primers and probes for SNP detection and gene expression profiling on multiple sequences in a single search run. Our customers, typically choose over 10,000 sequences at a time.  The highly specific, high-throughput capacity makes AlleleID® “best in class” for oligonucleotide synthesis.

3. SNP Detection. A Single Nucleotide Polymorphism (SNP) is the variation of a single base pair in the DNA sequence between either the members of a species or between the paired chromosomes of an individual. These polymorphisms may affect how organisms develop diseases and respond to chemicals and drugs. SNPs are, therefore, of great value in biomedical research and drug development. SNP detection and genotyping can be used to explain and diagnose many diseases, to study the variation in drug responses, to establish the origin of biological material and to study the relatedness between individuals. DNA microarrays represent a technological platform that enables SNP genotyping in a rapid and massively parallel manner. SNP primers and probes for Variation Identification Platform (VIP) microarrays and other genotyping applications are optimized by AlleleID® to afford optimal amplification efficiency and hybridization specificity.  AlleleID® designs both wild and mutant probes to amplify and genotype any allele of interest. AlleleID® is highly recommended for Arrayit VIP Genotyping Platform customers.  Thousands of SNPs for designing probes for SNP detection and genotyping can be loaded into AlleleID®. The SNPs can be defined as a variation feature in the GenBank file format. To load unpublished SNP information, you can reformat your sequence data to a GenBank like format with the help of the template provided, or you can add SNP information to sequences already loaded in a project with the “Add SNP” option. For SNP detection assays, use the “SNP at the center of probe” option to design wild and mutant probes. Probe output can be defined to design single or multiple probes as required. For multiple probes, you can specify the sense (sense or anti-sense) and the minimum distance between the probes.

4. Gene Expression Profiling. AlleleID® allows the design of thousands of specific oligonucleotides for microarray-based gene expression profiling in a single search run. Complete user control is available to alter the design parameters to meet specific research needs. You can batch BLAST sequences and avoid repeats and low complexity regions before designing sequences. The software includes automatic homology avoidance using BLAST searches of hundreds of sequences in a single search run. The results are automatically interpreted and the homologies identified are avoided during oligonucleotide design. Specificity checks include BLAST searches with primers and probes designed against all the genomic databases available at NCBI, including the redundant nr database to verify the specificity of design. Product location allows the user to specify the product length and product location at the 3’end, 5’end or anywhere in the sequence. Comprehensive selection criteria screen oligonucleotides for thermodynamic properties as well as secondary structure. Graphics for the structures are also displayed. Ranking uses statistical optimization techniques to design the best primer and probe for each template. A list of alternate designs is also available. A proprietary algorithm calculates oligonucleotide melting temperature (Tm) based on nearest-neighbor thermodynamics.

5. Whole Genome Microarrays. Whole genome microarray experiments use hybridization to scan the entire genome of an organism. The technology helps investigate expression levels of all genes, transcripts or a large fraction of the genome simultaneously with high reproducibility and sensitivity. One method of whole genome analysis uses a set of overlapping oligonucleotides covering the entire genome. The development of whole genome microaarray represents another advancement critical to the development of new microarraying applications. Whole genome microarrays have been useful for studying the poorly understood aspects of trancriptomes and natural antisense transcripts as they can simultaneously monitor gene expression on both strands of the genome. They have been found extremely useful for discovering novel genes. AlleleID® allows researchers to study the genetic make-up of entire organisms effortlessly by detecting every gene or exon in the whole genome. This enables easy discovery of differentially- and alternatively-spliced transcripts, SNPs, DNA sequence variation in individuals or populations and comparative genome hybridization (CGH). Whole genome microarray design is fast and easy. can be used to interrogate a gene, exon or any other stretch of DNA of your choice. Oligonucleotides can be designed by position to detect regions of interest in the entire genome. Oligonucleotides for equal-sized fragments divides the entire genome into equal sized fragments and designs sequences for each one of them. Sequences by annotations helps you design oligonucleotides for each exon or gene. The genes and exons are resolved using GenBank file annotations or can be specified manually.

6. Tiling Microarrays. You can print every nucleotide of a long genomic sequence using amplified material obtained from whole genome amplification and avoid repetitive regions. Designing microarrays to characterize regulatory elements, or to study epigenetic modifications, methylation patterns and protein binding sites is also straightforward using AlleleID®.

7. Re-sequencing Microarrays. AlleleID® allows the design of re-sequencing microarrays allowing the detection of SNP and other sequence variations in a large number of samples. One of the common challenges in re-sequencing microarray design is difficult base calls caused by inter-template cross hybridization. With the unique feature called project BLAST, you can identify and avoid the homologous regions that create false positives in re-sequencing.

Software Features

Probe and primer design

  • Choices in probe design: AlleleID® can design single or multiple probes per sequence for your microarray projects. Allows specifying the minimum distance between two probes to avoid overlapping.
  • Product Location: Allows specifying the product (amplicon) length and product location viz at the 3’end, 5’end or anywhere in the sequence.
  • Comprehensive selection criteria: Screens oligonucleotides for their thermodynamic properties as well as secondary structures. Graphics for the structures are also displayed.
  • Ranking: Uses statistical optimization techniques to design the best primer and probe for each template. A list of alternate designs is also available.
  • Algorithm: Calculates oligonucleotide Tm using nearest-neighbor thermodynamics.

BLAST search

  • Specificity Check: Thousands of searches are submitted automatically. Results are interpreted and displayed in the Homology Avoidance window.
  • Batch Sequence BLAST search: AlleleID® can BLAST search hundreds of sequences. The results are interpreted and the homologies identified are avoided while designing primers.
  • Local BLAST: AlleleID® can BLAST search against a custom local database that can be set up on a Unix machine using the WWW Standalone BLAST facility of the NCBI. Read the inbuilt product help for details.
  • 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.
  • Verification of specific design: The primers and probes designed by the program can be BLAST searched against all the nucleotide databases available at NCBI to verify the specificity of design.
  • Repeat regions: Optimizes BLAST search parameters to detect human repeats while searching the human RNA (previously called mRNA) database at NCBI.

SNP detection and genotyping

  • SNP loading: Easily add a single SNP at a time or load thousands of SNPs using standard GenBank variation files.
  • SNP Detection: Designs probes for SNP detection (both wild and mutant) with SNP at the center of the probe.
  • SNP genotyping with AlleleID®: Designs SNP genotyping probes with SNP or one base upstream of the 3' end of the probe.

Whole genome microarrays

  • By length: Probes can be designed for the fragments of a size chosen by the user. The sequence is broken down into small equal-sized fragments and then a specific probe is designed for each one of them.
  • By position: Probes can be designed on genes/fragments, the start and stop position for which can be  imported from a text file.
  • By annotation: Probes can be designed on genes or exons, the annotations for which can be read from the GenBank file.
  • BLAST to ensure specificity: For a whole genome sequence, AlleleID® automatically creates a local custom database of the input sequence and BLAST searches every fragment against it. To verify the specificity of design, you can BLAST the designed oligos.
  • Sequence size: AlleleID® can design probes spanning the entire genome of the organism. This ability is especially useful to study the expression of intergenic and intragenic regions. Fragments to be studied can be generated on the basis of their length, their position or by specifying an annotation such as gene, exon or both.
  • Uniform Tm values: AlleleID® designs probes free of secondary structures and with uniform Tm values ensuring a high rate of success of microarray experiments.

Tiling microarrays

  • Sequence size: AlleleID® can design tiling primers to study protein binding regions of small to medium sized genomes. You can generate both distinct or overlapping amplicons depending on the specificity desired.
  • Distinct amplicon: Primers are designed such that there is no overlap between adjacent amplicons.
  • Overlapping amplicon: Primers are designed such that the adjacent amplicons overlap each other in the flanking regions.
  • Whole Genome Amplification using AlleleID®

Re-sequencing microarrays

  • Resequencing probe design: In addition to standard probes, AlleleID® also designs re-sequencing microarrays. With custom re-sequencing microarrays, 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.
  • BLAST search: The challenge in designing chips for re-sequencing by hybridization is to achieve the lowest possible false positive rate. AlleleID® offers an innovative and unique project BLAST capability to identify these regions and recommends a multi-chip solution.
  • Avoiding repetitive regions: You can simply connect to the popular Repeat Masker using the handy link and AlleleID® will avoid creating spots that may generate false positives.

Computer Requirements
Arrayit strongly recommends BioBlue Computers for AlleleID® Software.  The recommended computer requirements are as follows:

  • AlleleID is supported by Windows XP, Windows 7, Windows 8, Windows 10 and has been tested on Macintosh OS 10.6-10.9
  • Pentium IV 1.8 GHz CPU
  • 1 GB of available RAM
  • 0.5 GB of available hard disk space
  • 800 X 600 screen resolution

Software Screenshots
Arrayit-AlleleID
Figure 1.
  AlleleID® is extensively integrated into ssequence databases.

microarray-software.3
Figure 2.
  AlleleID® allows analysis of oligonucleotide microarray parameters including length, melting temperture and GC content.

AlleleID-microarray
Figure 3.
  AlleleID® has a fluorescence resonance energy transfer (FRET) module for microarray comparisons.

Allele-ID
Figure 4.
  AlleleID® has advanced features that allow the alignment of multiple sequences for microarray applications.

AlleleID_software.1
Figure 5.
  AlleleID® empowers the design and analysis of molecular beacons for confirmatory microarray applications.

AlleleID-software
Figure 6.
  AlleleID® has sophisticated TaqMan® analysis capabilities for confimatory microarray applications.

Customer Feedback

"I used AlleleID to design a number of primers and they outperformed many of the published primers for similar pieces of target nucleic acid." -Dr. Graham W Burgess, James Cook University, Australia

"The primers that your program designed pretty much all worked to produce working taxa-specific primers with great efficiencies and R2 values on a standard dilution series to be used for qPCR. I really did enjoy the trial of AlleleID, what a great program!" -Mr. Ben Sutherland, University of Victoria, Canada.

"I designed multiplex TaqMan assay with 3 targets using AlleleID. Designing a multiplex assay using the software is quite easy and the results obtained are pretty good." -Dr. Hanneke de Valk, Director of ADD International bv, Netherlands.

"I really liked AlleleID, it's easy to work with and the site has a very nice design." -Ms. Josefine Hiller, Probi AB, Sweden.

"AlleleID has been of much help for designing primers for real time PCR. It has facilitated the work enormously." -Dr. Flavia M.Michelini, Universidad de Buenos Aires, Argentina.

"We bought the AlleleID® and so far I'm very happy with it. I designed species specific primers with AlleleID® (after having tried manually for some days) and the results are very good (really specific amplifications). That was for a sybr green detection. And I have to say the support team is really helpful when you face problems." -Ms. Cecile Thonar, ETH Zurich, Switzerland.

"AlleleID is extremely easy to use. I hardly needed to go through the tutorial and the Help section was so comprehensive that it answered all my questions." -Dr. Chantal Van Niekerk, University of Pretoria, South Africa.

"AlleleID was really helpful for my data. It has an easy interface."- Ms. Carolina Thompson, INTA, Argentina.

"I really liked AlleleID. I found it very useful and intuitive. I designed several sets of SYBR® Green primers using the software. I tested them and they all worked very well." -Dr. Jeannette Loram, Bermuda Institute of Ocean Sciences, Bermuda.

Technical Assistance
Please contact us if you have any questions, comments, suggestions, or if you need technical assistance. By electronic mail, use arrayit@arrayit.com and type "ArrayIt technical assistance" into the subject line. By email between the hours of 8AM and 8PM PST Monday through Friday. We want to hear about your successes and are always happy to feature contributed data on our website.

Recommended Products
H25K Whole Human Genome Chips
VIP Diagnostics Packages
Biomarker Discovery Services
BioBlue Bionformatics Computers
Nanoprint™ 2 Enterprise Level Microarrayers
Professional Series Microarray Printing Technology
SpotBot® 4 Personal Microarrayers
InnoScan® Microarray Laser Scanners
SpotLight™ Microarray Scanners
SpotWare™ Colorimetric Microarray Scanners

Scientific Publications
Click on the links to view recent scientific publications featuring Arrayit microarray products and software.

Ordering Information

Product

Description

Catalog ID

AlleleID® Microarray Software

Arrayit Corporation and Premier Biosoft collaborated to create AlleleID® oligonucleotide design software as the market's most advanced comprehensive solution for probe and primer design for microarray applications including gene expression, single nucleotide polymorphism (SNP) analysis, genotyping, whole genome analysis, tiling, re-sequencing, and many other applications in DNA and RNA microarrays. AlleleID® Microarray Software is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification. With ClustalW multiple sequence alignment at its core, AlleleID® can be used to design species identification/cross species probes for microarrays or real time PCR including SYBR® Green, TaqMan® MGB, TaqMan® probes, Molecular Beacons and real time PCR primers. AlleleID® also offers support for designing microarray experiments for detecting alternative splicing events.

ALID

AlleleID® Microarray Software Upgrade

Arrayit Corporation and Premier Biosoft collaborated to create AlleleID® oligonucleotide design software upgrade as the market's most advanced comprehensive solution for probe and primer design for microarray applications including gene expression, single nucleotide polymorphism (SNP) analysis, genotyping, whole genome analysis, tiling, re-sequencing, and many other applications in DNA and RNA microarrays. AlleleID® Microarray Software is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification. With ClustalW multiple sequence alignment at its core, AlleleID® can be used to design species identification/cross species probes for microarrays or real time PCR including SYBR® Green, TaqMan® MGB, TaqMan® probes, Molecular Beacons and real time PCR primers. AlleleID® also offers support for designing microarray experiments for detecting alternative splicing events.

ALIDU

 

Warranty

Arrayit life sciences products are sold for research purposes only. Arrayit brand products have been scientifically developed and are sold for research purposes. Extreme care and exact attention should be practiced in the use of the materials described herein. All Arrayit brand products are subject to extensive quality control and are guaranteed to perform as described when used properly. Any performance issues should be reported to Arrayit immediately. Arrayit’s liability is limited to the replacement of the product, or a full refund. Any misuse of this product is the full responsibility of the user, and Arrayit makes no warranty or guarantee under such circumstances. Pricing may vary up to 30% due to costs associated with distribution, import taxes, duties, customs clearance and shipping.

Mailing Lists
Shopping Cart
Your cart is empty.