[Biojava-dev] GSoC - File parsing coding exercise

[P. Troshin]

Hello David,

Welcome to BioJava! Ambiguous characters mean more than one amino acid in
protein sequence or nucleotide in DNA sequence.  Here is the list for DNA
sequences  http://en.wikipedia.org/wiki/Nucleic_acid_notation.

Good luck with your application,
Regards,
Peter



On 27 March 2012 21:01, David Felty <davfelty at gmail.com> wrote:

> Hello, BioJava!
>
> My name is David Felty, and I am a Computer Science student at Cornell
> University. Biology has always been one of my interests, and I've actually
> considered getting a degree in Bioinformatics; I feel like computer science
> has so much to offer the scientific fields. It is for this reason that I'm
> applying to BioJava for GSoC.
>
> I want to apply for the project entitled "New File Parsers for BioJava,"
> but I have a question about task 2 of the coding exercise at
> biojava.org/wiki/Coding_exercise. What are "ambiguous characters"? My
> guess, based on en.wikipedia.org/wiki/FASTA_format#Sequence_representation
> ,
> is that 'N', 'X', and '-' are ambiguous for nucleic acids, and 'X' and '-'.
> are ambiguous for amino acids. Is this correct?
>
> Thanks,
>
> David
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