There is a table of genes in mysql. I have a list of reg. elements, their start position on a chromosome, and their end position on a chromosome. How do you write a mysql command for perl program to search for the gene (from a table of genes downloaded in mysql) nearest each element. How do you make the perl program run faster since there are many elements for which you have to search for the nearest gene?
I am new to mysql and perl and have little programming background. Could you explain a little more? I must use a table of genes (that has over a 150K genes) that I downloaded into a mysql database. So i have a regulatory element and its start position, end position, and chromosome number. I have a table of genes. how do i match the gene closest upstream or downstream to this reg. element most easily? i will need to include a subroutine for finding the closest gene too. The thing I'm stuck on is how to find the closest gene.