bio-0.4.5: A bioinformatics library Source code Contents Index

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 aromatic :: AAProp hydrophobic :: AAProp polar :: AAProp small :: AAProp tiny :: AAProp charged :: AAProp negative :: AAProp positive :: AAProp aliphatic :: AAProp hydropathy :: Amino -> Double mass :: Amino -> Double strandP :: Amino -> Double helixP :: Amino -> Double

Documentation

type AAProp = Amino -> Bool Source

aromatic :: AAProp Source

hydrophobic :: AAProp Source

polar :: AAProp Source

small :: AAProp Source

tiny :: AAProp Source

charged :: AAProp Source

negative :: AAProp Source

positive :: AAProp Source

aliphatic :: AAProp Source

hydropathy :: Amino -> Double Source

mass :: Amino -> Double Source

strandP :: Amino -> Double Source

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.

helixP :: Amino -> Double Source

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