Finding nearby genes using MySQL query to the public server of USCS.
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes
Tag: genome
An insight about representing sub-sequence of numbers or range.
http://www.cs.utexas.edu/~EWD/ewd08xx/EWD831.PDF
Subsequence_of_numbers (PDF, local copy)
More discussions about the coordinate systems
http://biostar.stackexchange.com/questions/6394/what-are-the-advantages-disadvantages-of-one-based-vs-zero-based-genome-coordina
http://bergmanlab.smith.man.ac.uk/?p=36
0-based, half-open coordinate system or interbase coordinate system
| A | C | G | T | A | C | G | T | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8
So if you wanted to describe the first base, it would be:
chr 0 1
and GTAC:
chr 2 6
http://biostar.stackexchange.com/questions/7064/bed-coordinates
Update:
Interbase coordinates (top) and base-oriented (below) from Chado Wiki
