Question: extract predicted gene sequences from gilmmer output
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gravatar for akhilvbioinfo
4.4 years ago by
akhilvbioinfo140
India, chennai
akhilvbioinfo140 wrote:

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

myposts gene assembly genome • 1.4k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 4.4 years ago by akhilvbioinfo140
0
gravatar for zorbax
4.4 years ago by
zorbax30
Mexico
zorbax30 wrote:

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;"}'
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by zorbax30

thanks ..it works 

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by akhilvbioinfo140

it list out all predicted gene list...then how can i extract all predicted orf sequences ?

ADD REPLYlink written 4.4 years ago by akhilvbioinfo140
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