bio-0.5.3: A bioinformatics library

Safe HaskellSafe-Inferred



Functionality for manipulating KEGG annotations.

KEGG is a bit hard find, but there exist species-specific tables Available organisms are listed in the table at

Data for each organism is stored its own subdirectory under

Containing tables linking everything -- including external resources like UniProt, PDB, or NCBI -- together.



genReadKegg :: FilePath -> IO [(ByteString, ByteString)]Source

Most KEGG files that contain associations, have one association per line, consisting of two items separated by whitespace. This is a generalized reader function.

newtype KO Source


KO ByteString 


decodeUP :: ByteString -> UniProtAccSource

Convert UniProt IDs (up:xxxxxx) to the UniProtAcc type.

decodeKO :: ByteString -> KOSource

Convert KO IDs (ko:xxxxx) to the KO data type.

removePrefix :: String -> String -> (ByteString -> a) -> ByteString -> aSource

KEGG uses strings with an identifying prefix for IDs. This helper function checks and removes prefix to construct native values.