Genetic Code

In the News..

15-11-2006

CLC bio New Hardware Accelerator

CLCbio have created the ‘CUBE’. A hardware unit which runs Smith Waterman up to 125 times faster than a 3 GHz desktop computer.

Using the Cube instead of BLAST, improves the quality of the data you're working with! read more..
The Tommi Melon

Array Designer Features

PCR Primer and Probe Design

  • Automatic Homology Avoidance: Hundreds of sequences are BLAST searched. The results are automatically interpreted and the homologies identified are avoided during the design.
  • Specificity check: 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.
  • Product Location: Allows specifying the product length and product location viz at the 3’end, 5’end or anywhere in the sequence.
  • Comprehensive selection criteria: Screens oligos 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 oligo Tm using nearest neighbor thermodynamic algorithm.
  • Oligo Microarray design: Array Designer helps design highly specific probes for oligo microarray construction.
  • Probe design:Array Designer is a microarray software package to design thousands of specific oligonucleotide probes and cDNA primers for microarray projects
  • Multiple probes: Designs multiple probes per sequence for increased accuracy of detection. Allows specifying the minimum distance between two probes to avoid overlapping.
  • Microarray experiments are dependent on the quality of the microarray design. Array Designer not only designs high quality probes, but specially selects them for well matched Tm values.
  • Array Designer designs probes free of secondary structures and with uniform Tm values ensuring a high rate of success of microarray experiments.
  • Array Designer can design primers and probes for SNP analysis and SNP detection.
  • The default parameter values in Array designer are based on the experience of a number of labs doing microarray design.

SNP specific Primer and Oligo Probe Design with Array Designer

  • Single Nucleotide Polymorphism(SNP): A Single nucleotide polymorphism is represented by change of one nucleotide within the sequence of DNA strand. There are various type of studies performed for SNPs like SNP detection , SNP scoring , SNP mining for detection of genes affecting important diseases and economic traits
  • SNP loading: easily add a single SNP at a time or load thousands of SNPs using standard GenBank variation files.
  • SNP detection: SNP detection can be used to explain and diagnose many diseases , to study variation in drug responses to establish the origin of biological material and relatedness between individuals. DNA microarrays represent a technological platform that enables SNP detection in the area of pharmacogenetic diagnosis. The most popular method for SNP detection is sequencing but this method is more expensive and time consuming as compared to other microarray based methods.
  • NP Detection with Array Designer: Design SNP probes for both hybridization and primer extension detection PCR Primers.
  • SNP detection: Designs probes to span the site. Designs both wild and mutant probes.
  • SNP detection with primer extension: Designs probes located with their 3’end at the specified site.
  • SNP amplification: designs primers to amplify SNP sites.
  • SNP analysis: SNP Analysis compares the potential effects of single nucleotide polymorphism (SNP) associated with your sequence. Quantitative SNP analysis provides a powerful tool for the identification of novel tumor markers and for the characterization of genetic alterations in human tumors. Array hybridization method is used for SNP analysis which rely on the differences in hybridization stability of short oligonucleotides to perfectly matched and mismatched target sequence variants. Allele-specific oligonucleotide (ASO) hybridizations are frequently performed with either the DNA samples or the oligonucleotides arrayed on a surface.
  • SNP analysis with Array Designer: Performs SNP analysis for thousands of unpublished SNPs with single click of a button.
  • cDNA oligonucleotide array: Designs probes to be located anywhere within a region around the site. Allows design of multiple probes near the 3' end of the sequence for redundant cDNA detection.

Whole Genome Arrays

  • Sequence size: Array Designer 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.
  • 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, Array Designer 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.

Tiling Arrays

  • Sequence size: Array Designer 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.

Resequencing Arrays

  • Resequencing probe design: In addition to standard probes, Array Designer also designs 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 chips for resequencing by hybridization is to achieve the lowest possible false positive rate. Array Designer offers an innovative and unique project BLAST capability to identify these regions and recommends a multi-chip solution.
  • You can 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

  • Project BLAST: One of the vexing problems in resequencing array design is false base calls caused by inter-template cross hybridization. With the unique feature which we call project BLAST, you can identify and avoid the homologous regions that create false positives.
  • Simply BLAST search all the sequences of a 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.

BLAST

  • Specificity Check: Thousands of searches are submitted automatically. Results are interpreted and displayed in the Homology Avoidance window.
  • Oligo and Amplicon BLAST: The oligos designed by the program and the amplicon can be BLAST searched against any or all of the nucleotide databases available at NCBI.
  • 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 Array Designer to BLAST search your query sequence against them.
  • Uniform conditions: PCR primer design is optimized to amplify all sequences under uniform reaction conditions.
  • Custom databases: Works with custom databases saved locally using standalone WWW BLAST facility of NCBI.
  • Repeat regions: Optimizes BLAST search parameters to detect human repeats while searching the human RNA (previously called mRNA) database at NCBI.

Speed

  • Per sequence Processes a 10kb sequence in 2-3 seconds.
  • 10 minutes Processor approximately 300 10kb sequences in 10 minutes.

Data Management

  • Application Database Maintains a local database for sequence information and BLAST results.
  • Data management: Manages data of multiple users and multiple projects by creating a separate project for each.

Input / Output

  • File formats: Supports GenBank and FASTA formats. GenBank and FASTA formatted files can contain multiple sequences.
  • Unlimited templates Supports any number of templates in a single run.
  • Flexible output format: Outputs a tab delimited format ready for viewing and manipulating in any spread sheet program, or databases like Oracle or Access; or in synthesis order forms of a vendor of your choice.
  • Specify output: Allows control over primer and probe properties that are to be exported to the output file.