[Biojava-l] Detect seq?

Schreiber, Mark mark.schreiber at agresearch.co.nz
Wed Sep 17 18:03:01 EDT 2003

Hi Suman,

If you are trying to determine the Alphabet of a BJ Sequence or SymbolList you would say something like seq.getAlphabet().getName() which will return "DNA" or RNA etc.

Unfortunately there is not a good (fool proof) way to guess the sequence type from a "flat file" unless that file specifically says the type. Often you can infer it (ie GenBank is DNA, SwissProt is protein) but for Fasta you often cannot unless it contains a symbol not found in the DNA alphabet (including ambiguities).

- Mark

-----Original Message-----
From: Suman Kanuganti [mailto:bioinformatics4suman at yahoo.com] 
Sent: Thursday, 18 September 2003 9:20 a.m.
To: biojava-l at biojava.org
Subject: [Biojava-l] Detect seq?

Ok; is there any best method to tell what is the seq
type is in biojava? I mean is that a dna sequence or
protein sequence etc. 

I have seen SeqAlignReadWrite.guessFileType but this
is no approriate and does work,

Suman K

Suman K
BioInformatics Associate,
Genomics Research,
University of Missouri - Columbia.

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