Many types of arrays exist and the broadest distinction is whether they are spatially arranged on a surface or on coded beads:
* The traditional solid-phase array is a collection of orderly microscopic "spots", called features, each with thousands of identical and specific probes attached to a solid surface, such as glass, plastic or silicon biochip (commonly known as a genome chip, DNA chip or gene array). Thousands of these features can be placed in known locations on a single DNA microarray.
* The alternative bead array is a collection of microscopic polystyrene beads, each with a specific probe and a ratio of two or more dyes, which do not interfere with the fluorescent dyes used on the target sequence.
DNA microarrays can be used to detect DNA (as in comparative genomic hybridization), or detect RNA (most commonly as cDNA after reverse transcription) that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling.
Applications include:
Specialised arrays tailored to particular crops are becoming increasingly popular in molecular breeding applications. In the future they could be used to screen seedlings at early stages to lower the number of unneeded seedlings tried out in breeding operations.