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Array Designer

Upgrades

Array Designer 4.41 Released

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

Array Designer 4.40 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 and 64-bit Windows OS.

Array Designer 4.30 Released

The upgrade accommodates the changes at the NCBI BLAST server, support for all the genomic databases at NCBI and includes fixes to reported problems.

The upgrade offers compatibility with Windows 7.

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 accommodate 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).

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