[EMBOSS] getorf includes unspecified amino acids as part of the ORF sequence

[Peter Rice]

Hi Avi,

> The input is a simple fasta file with only A,C,T,G letters and
> nothing else, so I wouldn't expect any Xs. In addition, even if there
> would be Ns (and there are no Ns) the program cannot know if such Ns
> do not include stopcodons so it should not consider them as part of an ORF.

>>> 00001_3 [803 - 1120]
>> LARLRFVVLGNSFIASAKGWSTPYGPTTFGPFRSCIYPRVFRSTRVRKAMATRIGSNRVN
>> ILIRCTXXXXXXXXXXXXXXXXXXXXXXXXXNPYLGWWCYIFCIFR

That suggests the Xs have all come from stop codons.

There are other possibilities, including a badly formatted input file
(perhaps two sequences and descriptions read as one).

We do need to see the input file to know where those Xs are from.

Peter Rice