Blog about IUPAC codes

[kinow]

Maybe try to write a Java port of Biostrings using Apache Commons Text.

• https://en.wikipedia.org/wiki/Nucleic_acid_notation
• http://www.bioinformatics.org/sms/iupac.html
• https://bioconductor.org/packages/release/bioc/html/Biostrings.html

[kinow]

https://github.com/kinow/java-biostrings

[kinow]

http://www.chick.manchester.ac.uk/SiteSeer/IUPAC_codes.html

[kinow]

Not necessary to really blog about it.

[kinow]

In the end we can write the port of the basic classes without Text :-)

[kinow]

The draft that I started...

The R Biostrings library contains several classes to help manipulating strings
from different alphabets.

`XString` is the base class, with the following implementations:

* BString - used to store any string (B comes from "B"ig String)
* DNAString - used to store DNA sequence strings
* RNAString - used to store RNA sequence strings
* AAString - used to store Amino Acids sequence strings

You can store any string in a BString. But DNAString, RNAString, and the
AAString have a limited alphabet, defining the characters that you may use
when storing sequence strings.

 (A, C, G, T, M, R, W, S, Y, K, V, H, D, B, N, -, +, and . for the gap symbol)
* 

[kinow]

Using the AlphabetConverter or similar classes would be an overhead