I am looking for a reliable software or script which can send me back the coding genes in well annotated genomes (mouse, human etc...) that are upstream or downstream a genomic position. Do you know such kind of tool ?
the UCSC genome browser will show you your location and enlarging it the genes nearby (http://genome.ucsc.edu). therefore you can get what you'll see by its associated table browser (in tools).... you can configure the view and add/discard tracks as you want.
The question is more to do it automatically because I may have more than hundreds of positions to check at the same time, so I am looking for a script or a software.