dagLogo-package: Visualize significant conserved peptide sequence pattern in...

In jianhong/dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

Visualize significant conserved peptide sequence pattern in groups based on the probability theory

Description

dagLogo provides differential analysis of grouped/ungrouped amino acid usage between an input set of aligned peptide sequences and a background set of aligned peptide sequences which can be generated in different ways. Results of Fisher's exact test and/or Z-test are visualized using a heatmap or DAG Logo.

Details

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 unaligned amino acid sequences.

3. Except that random, regional (called anchored) and terminal (called restricted in dagLogo) background model built from the whole proteome, the background set could be generated using subsequences from regions of the protein sequences matching the input set and complementary set of the input set.

Author(s)

Jianhong Ou, Haibo Liu, Julie Lihua Zhu

Maintainer: Jianhong Ou <[e-mail]>

Examples

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

jianhong/dagLogo documentation built on Nov. 5, 2024, 7:46 a.m.