GFF FORMAT:

     $1     $2     $3     $4     $5     $6     $7     $8     $9
     seq   prog                                              gene
    name   name    exon   start   end   score  +/-    frame  group

GeneId: already in GFF format

Genscan:

gawk 'BEGIN{OFS="\t"}$2 ~ /Term|Intr|Init/ {print "AC012089", "genscan", $2, start=($4<$5 ? $4 : $5), end=($5<$4 ? $4 : $5), $13,$3,$7, $1}'  AC012089.genscan  | sed 's/\.[0-9][0-9]$//' > AC012089.genscan.gff 

Grail:

gawk 'BEGIN{OFS="\t"}$2 {print "AC012089","genscan", $9, start=($4<$5 ? $4 : $5), end=($5<$4 ? $4 : $5), $8,$2,$3}'  AC012089.grail2 | sed 's/\.[0-9][0-9]$//' > AC012089.grail2.gff 

GeneMark:

 gawk 'BEGIN{OFS="\t"}{print "AC012089", "GeneMark", "exo",  start=($1<$2 ? $1 : $2), end=($2<$1 ? $1 : $2),$7,$3,$5}' genemark24.cgi  | sed 's/\.[0-9][0-9]$//' > AC012089.gff