This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Eukaryotic gene prediction using GeneMark-ES

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?

gene prediction genemark
• 4,619 views • link
updated by lieven.sterck lieven.sterck • written by lakhujanivijay lakhujanivijay

1 answer

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)

• 0 views • link
written by lieven.sterck lieven.sterck

An alignment file in gff format sounds alien to me.

• 0 views • link
written by lakhujanivijay lakhujanivijay

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 .

• 0 views • link
written by lieven.sterck lieven.sterck

Log in to answer this question.

More posts like this