[Biojava-dev] GSoC - File parsing coding exercise

[Steve Darnell]

And here is a list of the IUPAC-IUB codes for the amino acids (26 characters): http://www.ebi.ac.uk/2can/tutorials/aa.html or http://en.wikipedia.org/wiki/Amino_acid#Table_of_standard_amino_acid_abbreviations_and_properties. There are many similar references all over the web, but J, O, and U are often missing.

Regards,
Steve

--
Steve Darnell
DNASTAR, Inc.
Madison, WI USA

-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of P. Troshin
Sent: Tuesday, March 27, 2012 4:00 PM
To: David Felty
Cc: biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] GSoC - File parsing coding exercise

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
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
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