<p>Suppose I have Protein1, Protein2, Protein3 that are expressed by Gene1, Gene2, Gene3. I want to know Gene1, Gene2, Gene3 in the genome sequence are neighbor or not?</p>

<p>Genome: ========Gene1=====Gene2=======Gene3======</p>

<p>I suggest you to sort your gff file according to scaffold (chromesome) firstly, and coordinate secondly. they sit at the first column and fourth column, repectively.</p>

<p>REF: http://asia.ensembl.org/info/website/upload/gff.html?redirect=no</p>
