Question: Exonerate Gff In Artemis
1
gravatar for Daniel Fernández
6.7 years ago by
Lima, Perú
Daniel Fernández40 wrote:

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?

deleted-post • 2.3k views
ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 6.7 years ago by Daniel Fernández40

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?

ADD REPLYlink written 6.7 years ago by Giovanni M Dall'Olio26k
1
gravatar for Daniel Fernández
6.7 years ago by
Lima, Perú
Daniel Fernández40 wrote:

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)

ADD COMMENTlink written 6.7 years ago by Daniel Fernández40

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.

ADD REPLYlink written 6.7 years ago by Giovanni M Dall'Olio26k

Ok, I did a new post, thanks

ADD REPLYlink written 6.7 years ago by Daniel Fernández40
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