Thanks so much for the detailed answer? Is there anywhere to learn more about this besides wikipedia? Every time I try to learn this I end up there and it confuses the bejesus out of me.
What are mate pairs? How does that help with sequencing?
What are mate pairs? How does that help with sequencing?
Mate-pairs are essentially reads taken from opposite ends of a single fragment of DNA. This is useful for de novo sequencing, where they act almost like a single, very long read. The problem with random sequencing (both shotgun sequencing and current "next-generation" sequencing technologies) is that it's not obvious how a given read relates to the other reads you have.
Using the jigsaw puzzle analogy, mate-pair sequencing is roughly equivalent to being told that a given piece is 8-10 pieces away from another piece in a given direction. You still won't necessarily know exactly where to put either of the pieces, but it narrows the search space hugely, especially when you have one in place.
[1] Mate Pair libraries: http://www.illumina.com/technology/mate_pair_sequencing_assa...
[2] Paired-end sequencing: http://www.illumina.com/technology/paired_end_sequencing_ass...