bio-0.5.2: A bioinformatics library

Safe Haskell | Safe-Infered

Bio.Sequence.AminoProperties

Description

Encodes a table of amino acid properties. Based on Livingstone & Barton, CABIOS, 9, 745-756, 1993, as seen at: http:www.compbio.dundee.ac.ukuserws-dev1jalviewlatesthelphtmlmiscaaproperties.html NB: based on the graphic, not the table (in which P is polar, but T is not) |

Synopsis

- type AAProp = Amino -> Bool
- oneOf :: [Amino] -> Amino -> Bool
- or :: (t -> Bool) -> (t -> Bool) -> t -> Bool
- aliphatic :: AAProp
- positive :: AAProp
- negative :: AAProp
- charged :: AAProp
- tiny :: AAProp
- small :: AAProp
- polar :: AAProp
- hydrophobic :: AAProp
- aromatic :: AAProp
- hydropathy :: Amino -> Double
- mass :: Amino -> Double
- helixP :: Amino -> Double
- strandP :: Amino -> Double

# Documentation

type AAProp = Amino -> Bool

oneOf :: [Amino] -> Amino -> Bool

or :: (t -> Bool) -> (t -> Bool) -> t -> Bool

aliphatic :: AAProp

positive :: AAProp

negative :: AAProp

charged :: AAProp

tiny :: AAProp

small :: AAProp

polar :: AAProp

hydrophobic :: AAProp

aromatic :: AAProp

hydropathy :: Amino -> Double

mass :: Amino -> Double

helixP :: Amino -> Double

The propensities for forming secondary structures From Zvelebil and Baum: Understanding Bioinformatics, Chapter 11 citing Chou and Fasman. Today, more complex methods like GOR are recommended instead.

strandP :: Amino -> Double

The propensities for forming secondary structures From Zvelebil and Baum: Understanding Bioinformatics, Chapter 11 citing Chou and Fasman. Today, more complex methods like GOR are recommended instead.