[maker-devel] Problem extracting fasta from a GFF file generated with MAKER

[Carson Holt]

You are probably getting the wrong proteins from your scripts because you
are not taking into account the 5' and 3' UTR in the transcript.

For example
>snap_masked-contig-processed-gene-0.2-mRNA-1 transcript offset:261 AED:0.25
eAED:0.25 QI:261|0.4|0.83|0.83|0.8|0.83|6|22|240

The 5' UTR is 261bp and the 3' UTR is 22bp long.  Both would have to be
trimmed before translating the transcript into a protein. Once they are
trimmed you can use frame 0 for the translation.

The fasta_tool that comes with MAKER can be used to quickly trim the UTR.

Example:
fasta_tool maker_transcripts.fasta --trim_maker_utr

Then you can try your other scripts again.

Thanks,
Carson


From:  Diana Garnica Moreno <diana.garnica at anu.edu.au>
Date:  Monday, March 24, 2014 at 5:11 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Problem extracting fasta from a GFF file generated
with MAKER

Hi there,



We recently assembled a fungal genome using MAKER and we got the gene
models. and the corresponding transcripts, predicted proteins and GFF files.
However, the predicted proteins do not have the stop codon included so I do
not know which proteins are complete and which ones are incomplete at the 3'
end. To solve that I have used different programs to extract the fasta
sequence of the CDSs given the gff file and the genome sequence. The problem
is that with the tools I have tested I get the right sequence for some of
the proteins and wrong sequences for others (with multiple stop codons for
example). I am not sure why it happens and since it happens with different
tools (different python scripts and even gffread from cufflink) I do not
know where is the problem. Could you please give me some advice on how to
extract the right sequences with the stop codons included?



Thanks!



Diana
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