[Bioperl-l] testing for sequence

[Heikki Lehvaslaiho]

Guoneng Zhong wrote:
> 
> Hi,
> Is there a way for me to know if a given string looks like a protein or
> dna/rna sequence?  Other than doing a grep on all the DNA and Protein
> symbols?

There is an internal method _guess_alphabet @ Bio::PrimarySeqI which is
called when you set the seq() method with your sequence string. It sets the
alphabet into dna/rna/protein depending on ([atgc]u? count / seq_length). If
the ration is above 85% then it is not a protein. This is heuristics but
works in most cases. You can always confuse this and almost any algorithm
with heavy use of ambiguous nucleotide characters.

	-Heikki




> G
> 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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