Design of a whole genome Drosophilia chip

The design files are available to the public. If you use our files or programs in your work then please cite NIH grant 5R24GM065513

A poster that we presented at the Indiana Bioinformatics conference in May 2004 is available in GIF and PNG formats.

There have been three designs done for the chip. Version 1 was done outside of Purdue; we analyzed the chip design. Version 2 was Purdue's initial design. Version 3 -- in progress -- is a revised design by Purdue.

The following links represent our work for the past 8 months.

Version 1 analysis done in June & July, 2003 plus a subsequent one done in late July, 2003. As part of this analysis we did a preliminary match to flybase.

Version 2 design finished in Nov., 2003. The annotation is a CSV (comma seperated) file suitable for upload into Excel or SAS. To go along with the annotation is a Fasta-format file of the original source sequences. There is a description (PDF) of the design process and a flowchart (PDF)

The Version 3 design is complete. There were many design files involved. The processing steps are complex. The final data [20773 probes including 5 negative controls] is available in FastA and CSV form. The CSV file has additional information that the FastA file does not contains.
Since they came from various source files, the probe names are mixture of nomenclatures. But they all follow the convention of 'A_B_C|P' where 'A', 'B' and 'C' are gene names and 'P' is the position. In the example there are 3 genes that made up a common region from which the probe was created. Most probes will come from a single gene and thus will have the form 'A:P'. A handful of genes (or clusters) have more than one probe created for them; the position number differentiates between these probes. Examples of gene names: 'CG3856-PB', 'gi|41618549|tpg', 'negative-control-7', etc.

Agilent Annotation Program - Get latest auto-generated annotations as well as the generator of these annotations.