Annotation In Gff3

Question

[Daniel Fernández]

Hi,

Can anybody tell me a program to find genes by homology that generate GFF3?

I tired AAT but only show me a table

I tried Exonerate but it give me a GFF2 and it can't load in artemis

If anybody tell me MAKER, yes it is very very useful, I tried to install it but it's very complicate for me, I tried to install it for 2 months and nothing.

And I read that is not recommended convert GFF2 to GFF3.

Can anybody help me, please?

Thanks

DNL

[Zev.Kronenberg]

People in the Maker community are friendly. You should ask for help. Where are you stuck? My lab developed Maker. Maybe I could help you get it up and running.

[Daniel Fernández]

Well, 5months ago I tried to install it. I remember that I can't install the RMBlast, I copy the executables in my $PATH, I run it and ok, but the maker did not recognize it, and I am confused because RMBlast have several binaries with the same name that Blast, so in my path I had binaries with the same name (no in same directory), and this is only one because some programs I can't install by the ./Build install, and when I installed these programs manually the maker did not recognize.

[Daniel Fernández]

I trying to install MAKER again, in RepeatMasker wich RepBase is the one I have to download?RepBase17.05.embl.tar.gz or RepBase17.05.fasta.tar.gz.

[Zev.Kronenberg]

Let me check with my lab-mate tomorrow morning and get back to you. I am on Mountain time.

[Zev.Kronenberg]

I think it is the EMBL file. I checked in my local install of maker and that's what I found in the RepeatMasker/Libraries directory.

[Daniel Fernández]

Well it is the libraries not the RepBase, http://www.girinst.org/server/RepBase/index.php, I downloaded both RepBase17.05.###.tar.gz, but I don't know how install it, it doesn't have a readme or install file.

Answer 1

[Christian]

genBlastG can produce GFF3 output.

genBlastG: using BLAST searches to build homologous gene models.

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

Answer 2

[Ryan Thompson]

The Cufflinks suite includes a program called "gffread" that can convert GFF2 (also know as GTF) to GFF3 and vice versa. As long as your GFF2 file is well-formed, it should convert OK to GFF3. It should be worth a try.

[Daniel Fernández]

I search in Cufflinks but I did not find the "gfftool", can you send me the link, please?

[Ryan Thompson]

Oops, it is actually called "gffread". I have edited my answer.

[Daniel Fernández]

I run the "gffread" but it show me an error: No such file or directory at ./gffread.pl line 27.

The line 27 is: open CONFIG, "/usr/users/ga002/corpasm/workarea/ricinus/conf/gffread.conf" or die $!;

[Ryan Thompson]

Are you using an old version of Cufflinks? In the current version, gffread is a compiled executable, not a Perl script.

[Daniel Fernández]

Sorry but what parameter I have to use to convert gff3 to gff2? I tried but without success

[Ryan Thompson]

Do you want to convert GFF2 to GFF3 or the reverse? The default is to output GFF3, and the -T option makes it output GFF2. Please read the help test for more information.

[Daniel Fernández]

Sorry, GFF2 to GFF3, I tried with

gffread -E exonerate.gff2 -o out.gff3

but it doesn't work, the outgff3 size is 0 , I tried tha same but with the augustus.gff3, and work, what's the problem?

[Ryan Thompson]

That looks like the right usage. I'm not sure what the problem is. Check for any error messages produced.

[Daniel Fernández]

No error message was produced, nothing, it's very rare. Before you test the gffread with exonerate.