README.fly
========== 

There are three files: 


1. pgenes.all.gff is a GFF as follows: 
$1 = chromosome label (dmel_1_ = 2L arm; 
                       dmel_2_ = 2R arm; 
                       dmel_3_ = 3L arm; 
                       dmel_4_ = 3R arm; 
                       dmel_5_ = chr 4 ; 
                       dmel_6_ = chr X ) 
$2 = (fasty) 
$3 = (match) 
$4 = start coord
$5 = end coord 
$6 = (.)
$7 = sense (+ or -)
$8 = (.) 
$9 = (Match) 
$10 = Name 
$11 = start of match in flybase sequence 
$12 = end of match in flybase sequence 


2. pgenes.all.fasta contains the sequences in 
fasta format 

>Name 
....sequence... 


3. pgenes.mapped.R3.gff is a GFF (see 1 above for legend)

An initial remapping of the pseudogenes onto Release 3 of the genome.