Question: Artemis Or Apollo
1
gravatar for Daniel Fernández
6.2 years ago by
Lima, Perú
Daniel Fernández40 wrote:

Hi, I have some very simple questions,

  • Is possible to load the Exonerate's output (GFF2) in Artemis ?

    ... I trying with some scripts and exe to convert but without success (processexonerategff3fast.pl; gffread)

  • If the first question is not. Can Apollo load GFF2 and/or GFF3?

    ... I trying to install apollo but I have some errors in the installation

  • Or ... Can you tell me another program to predict genes by homology, and which format is the output, GFF2 or GFF3, please please please?

    ... I've desperate, I posted here before but still I can not visualize my annotation format.

Please, any help.

=======================================================================

Hi Zev, I use the script that you tell me, but it show a little error, "gff_version|gf|v|:s",

$ exonerate -q Scaffold.fa -Q dna -t krt.fa -T dna -m e2g --refine region --showtargetgff yes --ryo ">%qi length=%ql alnlen=%qal\n>%ti length=%tl alnlen=%tal\n" > out.exonerate
$ ./process_exonerate_gff3.pl -t EST out.exonerate > out.gff
Error in option spec: "gff_version|gf|v|:s"

I add "-gf 3" and in othe order I add "-gff_version 3" and they both display the same error. can you help me

gff3 • 1.8k views
ADD COMMENTlink modified 6.2 years ago by Zev.Kronenberg11k • written 6.2 years ago by Daniel Fernández40

See edits below

ADD REPLYlink written 6.2 years ago by Zev.Kronenberg11k

Sorry, I'm not good in that, I tried with "fix_exhon -gf 2" and it show me the same error.

ADD REPLYlink written 6.2 years ago by Daniel Fernández40

Send me the new exonerate output file. Same email.

ADD REPLYlink written 6.2 years ago by Zev.Kronenberg11k
1
gravatar for Zev.Kronenberg
6.2 years ago by
United States
Zev.Kronenberg11k wrote:

Apollo is designed to look at gene annotations and can take gff3. I could help you bring your annotation file up to gff3 spec. That is if you are willing to share it.

Okay, after looking at your output I think you may need to do a little tweaking to get your data in a format that can be viewed.

You want to use this script: Gmod GFF3 exonerate.

The guys over at Gmod have their act together and I think this is the easiest solution.

However exonerate must be run with the settings below:

    −−showtargetgff yes
    −−ryo ">%qi length=%ql alnlen=%qal\n>%ti length=%tl alnlen=%tal\n"

  perl fix_exhon -gf 2 ~/Downloads/exonerate.gff > t.gff3
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Zev.Kronenberg11k

yes, thanks, do I give you my output gff2? or how to

ADD REPLYlink written 6.2 years ago by Daniel Fernández40

If it is small you can email it to zev.kronenberg [at] gmail.com. If it is larger you can create a drop box. Also just for piece of mind: I have no intention to distribute or use these data.

ADD REPLYlink written 6.2 years ago by Zev.Kronenberg11k

thanks I will send you by mail my gff2.

ADD REPLYlink written 6.2 years ago by Daniel Fernández40

Hi, I sent my gff2 by mail on Saturday, I hope you have received.

ADD REPLYlink written 6.2 years ago by Daniel Fernández40

Yes, I am playing with it now.

ADD REPLYlink written 6.2 years ago by Zev.Kronenberg11k

see edits above

ADD REPLYlink written 6.2 years ago by Zev.Kronenberg11k

Hi, thanks for the script, it show me a little error, see above

ADD REPLYlink written 6.2 years ago by Daniel Fernández40
1
gravatar for JC
6.2 years ago by
JC6.8k
Mexico
JC6.8k wrote:

Is possible to load the Exonerate's output (GFF2) in Artemis ?

You can try to convert the file with biopython: http://biopython.org/wiki/GFF_Parsing

If the first question is not. Can Apollo load GFF2 and/or GFF3?

Apollo can read both -> http://apollo.berkeleybop.org/current/userguide.html#ReadingGFF

Or ... Can you tell me another program to predict genes by homology, and which format is the output, GFF2 or GFF3, please please please?

Augustus http://bioinf.uni-greifswald.de/augustus/ can produce GFF3 and it's a really good gene predictor (you can use the homolog genes as "hints").

ADD COMMENTlink written 6.2 years ago by JC6.8k

Now I was trying with augustus, but the result doesn't convince me, because the homology.out.gff is very similar to the abinitio.out.gff, mmm ... this biopython, how I can install the modules? because there said that is not yet integrated to biopython, so I guess I only need this modules.

from BCBio import GFF

from Bio import SeqIO

ADD REPLYlink written 6.2 years ago by Daniel Fernández40
1
gravatar for Christian
6.2 years ago by
Christian2.6k
Cambridge, US
Christian2.6k wrote:

Have you looked at genBlastG? It can produce GFF3 output.

genBlastG: using BLAST searches to build homologous gene models.

Bioinformatics (2011) 27 (15): 2141-2143.

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Christian2.6k
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