Tool:Fungal genome annotation

Question

[bioinformaticssrm2011]

I want to annotate the fungal genome which I got from 454. For that I have predicted the genes using AUGUTUS tool (I have now a output file in gff format) using command-

augustus --species="Homo sapiens" --UTR=on 454AllContigs.fna > output.gff

Now I have gff file, now how can I use this file for annotation. Should I use other tools for annotation?

Best!

Shashank

[dago]

There are many other posts on this topic in the forum.

Answer 1

[matt.sarrasin]

Stajich's lab does fungal genome annotation and they use a pipeline that includes PASA. I've never tried it though, but it seems to work quite well for them.

I've been using MAKER for annotating my fungal species (using RNA-Seq data) and it's worked really well so far. You can feed your gff model directly into it and it'll annotate the genome using a bootstrap gene prediction re-training method.

[bioinformaticssrm2011]

I have installed the MAKER tool, now which command should i use as a for fungal genome annotation?

I am not able to find any workflow available for MAKER (fungal genome annotaion) as we can see in MOTHUR/QIIME.

So, can you tell me the commands which I can use for fungal genome annotation, as you have done work on MAKER.

[matt.sarrasin]

Here's a great tutorial on how to get it running.

And here's further explanation of the config files to control what's happening under the hood.

That should give you enough information to get you up and running, and to tweak it to your needs.

[bioinformaticssrm2011]

I tried to follow MAKER, I got an error, I used command (NOTE: i have only fungal genome in fasta format)-

qiime@qiime-VirtualBox:~/Desktop/maker/src$ which maker
/home/qiime/Desktop/maker/bin/maker

qiime@qiime-VirtualBox:~/Desktop/maker/src$ maker -CTL

qiime@qiime-VirtualBox:~/Desktop/maker/src$ genome=454AllContigs.fna
qiime@qiime-VirtualBox:~/Desktop/maker/src$ organism_type=eukaryotic
qiime@qiime-VirtualBox:~/Desktop/maker/src$ est_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ atleast_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ altest_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ protein_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ rm_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ model_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ pred_pass=1
qiime@qiime-VirtualBox:~/Desktop/maker/src$ other_pass=1
qiime@qiime-VirtualBox:~/Desktop/maker/src$ maker
STATUS: Parsing control files..
WARNING: blast_type is set to 'ncbi+' but executables cannot be located
The blast_type 'ncbi' will be used instead.

ERROR: You have failed to provide a value for 'genome' in the control files.

-->; rank=NA, hostname=qiime-VirtualBox

[matt.sarrasin]

Judging from what I see in your terminal output, it's as if you defined the genome, organism_type, etc. as variables in your shell, rather than in the maker_opts.ctl file. The maker_opts.ctl file is what you're looking to modify because it points Maker to the input files/settings.