Question: extract predicted gene sequences from gilmmer output
0
gravatar for akhilvbioinfo
2.1 years ago by
akhilvbioinfo100
India, chennai
akhilvbioinfo100 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 • 702 views
ADD COMMENTlink modified 16 days ago by Biostar ♦♦ 20 • written 2.1 years ago by akhilvbioinfo100
0
gravatar for zorbax
2.1 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 2.1 years ago • written 2.1 years ago by zorbax30

thanks ..it works 

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by akhilvbioinfo100

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

ADD REPLYlink written 2.1 years ago by akhilvbioinfo100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 838 users visited in the last hour