Due to the complexity of genes in most metazoan species, creating ALEXA designs can be a time consuming and computationally intense exercise. For species such as human the design process requires the creation of a very large number of probes to profile all exons, introns, exon-junctions and exon-boundaries. Testing the specificity and thermodynamic properties of such a large number of sequences can be a challenge for centres that do not have convenient access to substantial computational resources (a 'Beowulf' style cluster for example). For this reason and others it may be desirable to simply download a completed design for the species of interest. To date we have generated such designs for ten EnsEMBL genomes. Some summary statistics and links to related materials are provided for each of these below. Each of these designs was created using the same parameters as those used in our validation experiments in which arrays were manufactured for our designs using the NimbleGen platform and hybridized with their 50-mer hybridization protocol (originally designed for CGH arrays). Alternate array manufacturers are listed below.
If you are interested in a design not represented below (alternate species or design parameters) and you do not have access to the bioinformatic or computational resources neccessary to use the ALEXA platform, please Contact Us.
The designs described below are not specific to any particular array manufacturer. Once you have finalized your design, the actual microarrays can be printed or synthesized on numerous platforms. We used NimbleGen because they allow variable probe lengths and a density of 385,000 features on a single array. Other possibilities include Affymetrix, Agilent, IDT, Illumina, Operon, SuperArray, The Scripps Research Institute, etc.
Species: Caenorhabditis elegans
Species: Canis familiaris
Species: Drosophila melanogaster
NOTE: This design was used for Validation experiments
Species: Mus musculus
Species: Pan troglodytes
Species: Rattus norvegicus
Species: Saccharomyces cerevisiae
The images depicted for each species above were taken from the corresponding EnsEMBL build. For more details on the input EnsEMBL build used to generate each design follow the 'Source EnsEMBL Database' link for the species of interest or visit the EnsEMBL home page and find the appropriate species and version