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

[Diana Garnica Moreno]

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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