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Tool: Fungal genome annotation

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

genome sequencing
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updated by Ram Ram • written by bioinformaticssrm2011 bioinformaticssrm2011

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updated by Ram Ram • written by dago dago

1 answer

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.

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updated by Ram Ram • written by ka6AjxQY ka6AjxQY

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.

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updated by Ram Ram • written by bioinformaticssrm2011 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
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updated by Ram Ram • written by bioinformaticssrm2011 bioinformaticssrm2011

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.

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updated by Ram Ram • written by ka6AjxQY ka6AjxQY

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