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
•
written
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Daniel Fernández •
genBlastG can produce GFF3 output.
genBlastG: using BLAST searches to build homologous gene models.
Bioinformatics (2011) 27 (15): 2141-2143.
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.
I search in Cufflinks but I did not find the "gfftool", can you send me the link, please?
Oops, it is actually called "gffread". I have edited my answer.
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 $!;
Are you using an old version of Cufflinks? In the current version, gffread is a compiled executable, not a Perl script.
Sorry but what parameter I have to use to convert gff3 to gff2? I tried but without success
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.
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?
That looks like the right usage. I'm not sure what the problem is. Check for any error messages produced.
No error message was produced, nothing, it's very rare. Before you test the gffread with exonerate.
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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.
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.
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.
Let me check with my lab-mate tomorrow morning and get back to you. I am on Mountain time.
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.
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.