[Biojava-dev] BioJava FastaReader to read lower-case fasta sequences

[Scooter Willis]

Andreas

Easy to support upper/lower case. This goes to the PTM representation for
the GSOC work. 

I am proposing the following.

capC =Carboxamidylmethyl Cysteine
pmC' = Palmytoylated Cysteine
dsbC = Disulfide-bonded Cysteine
oM = Oxidized Methionine
pS = Phosphorylate Serine
pT = Phosphorylated Threonine


Etc

Where the following would be parsed creating a protein sequence from a
string

 DE[pS]TSW[oM]P would be parsed to the correct Protein Sequence for mass
and chemical composition. It should also survive protein sequence
alignment with protein sequences that do not have the same PTM.

Scooter











On 7/24/11 6:03 AM, "Andreas Prlic" <andreas at sdsc.edu> wrote:

>Hi,
>
>having a flag to convert all lower case to upper case should be only a
>small patch. I guess another question related to this is what
>approaches other people have taken to encode chemically modified
>residues in sequences in the most user friendly way. Any
>recommendations?
>
>Andreas
>
>
>
>On Fri, Jul 22, 2011 at 10:32 PM, Chuan Hock Koh <kohchuanhock at gmail.com>
>wrote:
>> Hi all,
>>
>> I realized that BioJava FastaReader would discriminate between upper and
>> lower cases and throws CompoundNotFound error when the input file
>>contains
>> protein sequences in lower case.
>>
>> I am wondering if it is possible to have a boolean to indicate whether
>>case
>> should be ignore in the Constructor.
>>
>> Thanks,
>> Chuan Hock Koh
>>
>> --
>> 
>>http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.com
>>p.nus.edu.sg/~ChuanHockKoh/index.html>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>_______________________________________________
>biojava-dev mailing list
>biojava-dev at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biojava-dev