Question: Eukaryotic gene prediction using GeneMark-ES
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gravatar for lakhujanivijay
2.1 years ago by
lakhujanivijay4.7k
India
lakhujanivijay4.7k wrote:

I am using GeneMark-ES Suite version 4.33 for Eukaryotic gene prediction for plant genome and I am kind of stuck

command

perl gmes_petap/gmes_petap.pl --evidence protein.fa  --cores 40 --sequence genome_assembly.fa --ET transcripts.gff

input files

protein.fa = a multi-fasta file having amino acid sequences from a closely related plant

genome_assembly.fa = genome assembly multi-fasta file having scaffold sequences for which I want to predict the genes

transcripts.gff = gff file for transcript sequences


error message

error, unexpected format found on line: >prot.1

error on call: /gmes_petap/reformat_gff.pl --out data/evidence.gff  --trace info/dna.trace  --in protein.fa  --quiet

I think I am providing a wrong file in the --evidence parameter as shown below

--ET           [filename]; to run training with introns coordinates from RNA-Seq read alignments (GFF format)
--evidence     [filename]; to use in prediction external evidence (RNA or protein) mapped to genome

What could (RNA or protein) mapped to genome possibly mean? Any ideas?

genemark prediction gene • 1.5k views
ADD COMMENTlink modified 2.1 years ago by lieven.sterck6.9k • written 2.1 years ago by lakhujanivijay4.7k
0
gravatar for lieven.sterck
2.1 years ago by
lieven.sterck6.9k
VIB, Ghent, Belgium
lieven.sterck6.9k wrote:

Not an expert in using GeneMark myself but I'm guessing it assumes some kind of alignment file (in gff format) of the proteins to the genome, and thus not a protein fasta file (which you apparently are providing)

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by lieven.sterck6.9k

An alignment file in gff format sounds alien to me.

ADD REPLYlink written 2.1 years ago by lakhujanivijay4.7k

well, I meant alignment as in 'HSP coordinates of aligned proteins to the genome' ( obtained by using eg. blast (not recommended), GenomeThreader, GeneWise ... ). apologies for the brevity .

ADD REPLYlink written 2.1 years ago by lieven.sterck6.9k
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