What is paired-end/mate pair sequencing?

The use of the terms "paried end" and "mate-pair" differ slightly for the 454 and Illumina technologies. For Illumina sequencing, a pair of reads coming from each end of the same contiguous DNA molecule are called "paired end" reads, and the distance between the two ends is user-definable within the range of 100 - 500 bp. The term "mate pair" describes pairs separated by a greater distance (typically 2 or 5 kb). Originally spaced by 2 -5 kb, these template molecules have been circularised, juxtaposing the ends, allowing sequencing of the ends of the original molecule in a small construct. Both paired end and mate pair libraries thus produce similar data (paired reads originating from the same template molecule and separated by a known distance) but their different construction method and insert length gives them their differing names. For 454 technology, the terms "paired end" and "mate-pair" are used interchangeably, and the library construiction process involves circularisation and juxtaposition of the ends of long molecules, similar to the mate-pair constructs used with Illumina technology. For 454 GS FLX, pair distances are typically 3kb, 8-10kb or 20kb.