Exonerate Gff In Artemis

Question

[Daniel Fernández]

Hi,

Maybe this is very simple question, I'm beginner in bioinformatics.

I'm trying to run exonerate. I tested with a partial chr1 of A. thaliana, and extracting its mRNA, only for testing. I generate the GFF of the query, the partial chr1, and the GFF of its genes, but when I try to load in artemis, it doesn't work, when I load the GFF, query or target, it only shows the partial chr1 fasta.

It is not a problem with artemis, because I load the augustus ab-inito.GFF and it works.

These are my commands:

exonerate -q At.chr1.fa -Q dna -t At.genes.fa -T dna -m e2g --refine region --showalignment no --showvulgar no --showquerygff yes > At.chr1.gff
exonerate -q At.chr1.fa -Q dna -t At.genes.fa -T dna -m e2g --refine region --showalignment no --showvulgar no --showtargetgff yes > At.genes.gff

artemis At.chr1.fa + At.chr1.gff                # only shows At.chr1.fa
artemis At.chr1.fa + At.genes.gff                # only shows At.chr1.fa
artemis At.chr1.fa + At.chr1.gff + At.genes.gff    # only shows At.chr1.fa

This is the At.chr1.gff

# --- START OF GFF DUMP ---
##gff-version 2
##source-version exonerate:est2genome 2.2.0
##date 2012-06-07
##type DNA
# seqname source feature start end score strand frame attributes
gi|332189094|gb|CP002684.1|    exonerate:est2genome    similarity    1838    2300    2315    +    .    alignment_id 1 ; Target mRNA1 ; Align 1838 1226 463
# --- END OF GFF DUMP ---

And this is the At.genes.gff

# --- START OF GFF DUMP ---
##gff-version 2
##source-version exonerate:est2genome 2.2.0
##date 2012-06-07
##type DNA
# seqname source feature start end score strand frame attributes
mRNA1    exonerate:est2genome    gene    1226    1688    2315    +    .    gene_id 1 ; sequence gi|332189094|gb|CP002684.1| ; gene_orientation .
mRNA1    exonerate:est2genome    exon    1226    1688    .    +    .    insertions 0 ; deletions 0
mRNA1    exonerate:est2genome    similarity    1226    1688    2315    +    .    alignment_id 1 ; Query gi|332189094|gb|CP002684.1| ; Align 1226 1838 463
# --- END OF GFF DUMP ---

Sorry for this question but how can I upload it in that link?

[Giovanni M Dall'Olio]

the query seems to be fine. Can you post the first few lines from the gff file that you get from exonerate? Why don't you try uploading it as a custom track to http://atensembl.arabidopsis.info/Arabidopsis_thaliana_TAIR/index.html , and see if it works?

Answer 1

[Daniel Fernández]

Well, maybe I found the problem, exonerate generate GFF2 and augutus generate GFF3. Maybe artemis doesn't accept GFF2, I read that is not recommended convert GFF2 to GFF3 so: Anybody tell me other program to findind genes by homology and generate GFF3 (if sombody tell me MAKER, yes its is very very usefull, I tried to install it, but its very dificult for me, I tried for 2 months and nothing)

[Giovanni M Dall'Olio]

ok, nice that you have found the answer and posted it here, so it may be useful to other people in the future. For the other matter, I recommend you to open a new question, you will get more answers.

[Daniel Fernández]

Ok, I did a new post, thanks