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I have some very short protein sequences that EM...

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I have some very short protein sequences that EMBOSS thinks are nucleic sequences. How do I force EMBOSS to treat them as nucleic acid sequences?

For example:

   > cat seq1
   > cat seq2

   % water seq1 seq2 -stdout -auto
   Smith-Waterman local alignment.
   An error has been found: Sequence is not nucleic

Here, 'water' automatically (and wrongly) thinks that A is adenosine instead of alanine and fails when it reads in seq2 and expects to find another nucleic acid sequence - but 'I' is not a valid base and so it fails.

A) For many sequence formats there is no way to specify the sequence type in the file, so EMBOSS has to guess.

There is a flag that can force EMBOSS programs to treat sequences as nucleic or protein.

   'water -help -verbose'

shows the full list of sequence qualifiers.

If you follow the sequence USA with '-sprotein' EMBOSS will check that it is a valid protein sequence.

If you need to force a sequence to be DNA, the qualifier is '-snucleotide'

The qualifier must follow the sequence to apply to one sequence, or can go at the start of the command line to refer to all sequences, for example:

   'water -sprotein seq4 seq3 -stdout -auto'

You can also use '-sprotein1' anywhere on the command line to refer to the first sequence and '-sprotein2' to refer to the second sequence.

Of course, like all EMBOSS qualifiers, you can shorten them so long as they are still unique. In this case, '-sp' and '-sn' will work (or '-sp1' and '-sp2' if you need the numbers).

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