dagLogo (version 1.10.2)

dagLogo-package: Visualize significant conserved amino acid sequence pattern in groups based on probability theory

Description

We implement iceLogo by R to visualize significant conserved amino acid sequence pattern based on probability theory. Compare to iceLogo, dagLogo can also visualize significant sequence patterns by clustering the peptides by groups such as charge, chemistry, hydrophobicity and etc.

Details

Package:

dagLogo

Type:

Package

Version:

1.0

Date:

2013-09-31

License:

GPL (>= 2)

DAG: Differential Amino acid Group

There are several differences between dagLogo from iceLogo:

1. The sequence patterns can be grouped by charge, chemistry, hydrophobicity and etc.

2. dagLogo accepts different length of aligned amino acid sequences.

3. Except Random, regional (called restricted in dagLogo) and terminal (called anchored) background model, the background sequence could be set to other regions of the genes in inputs and complementary set of the proteome.

Examples

    data("seq.example")
    data("proteome.example")
    bg <- buildBackgroundModel(seq.example, proteome=proteome.example, permutationSize=10L)
    t <- testDAU(seq.example, bg)
    dagLogo(t)