extract predicted gene sequences from gilmmer output

Question

[Eva_Maria]

I got two files from glimmer .detail and .predict...then how to extract all predicted genes sequence from these files?

Answer 1

[zorbax]

You can use http://dawgpaws.sourceforge.net/man/cnv_genemark2gff.html (this is for GeneMark)

For glimmer:

grep ^orf output.glimmer | awk '{OFS="\t"}{strang = "+"}{if($4 < 0) strang="-"}{gsub(/[+-]/," ")}{print "FASTA_HEADER", "GLIMMER", "gene" , $2 , $3, $5, strang , $4, "ID="$1"; NOTE:GLIMMER ORF prediction;"}'

[Eva_Maria]

Thanks, it works

[Eva_Maria]

It lists out all predicted gene list. Then how can I extract all predicted orf sequences?