Re: What exactly is crossing over and how is it used to determine chromosome sequence?

Hi Lucinda - Sorry I am a little slow in responding to your question.  Hope 
this is still in time to help you out.  
"Crossing over" is a fascinating phenomenon that takes place during germ 
cell formation.  During meiosis, the paired chromosomes exchange 
corresponding pieces with each other.  This causes a shuffling of genes 
between members of the chromosome pairs, so that genes inherited from the 
mother will end up on the same chromosome as genes inherited from the father 
once germ cell formation is complete.  This has been used extensively to map 
genes in lower animals such as the fruit fly and leads to the concept of 
linkage analysis in humans and other higher animals.

I'll refer you to a web site that gives a very nice explanation of the 
phenomenon and how it's used in mapping:
 http://library.thinkquest.org/18258/chromosome.htm

Also, check out a book entitled "Time, Love, Memory: A Great Biologist and 
His Quest for the Origins of Behavior", by Jonathan Weiner.  This has an 
excellent description of the phenomenon of crossing over as well as an 
historical account of its discovery by the great fly geneticist T.H. Morgan 
and his student Alfred Sturtevant.