Log-odds sequence logos

Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space

(2013) Viet-An Nguyen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

pLogo: a probabilistic approach to visualizing sequence motifs

(2013) Joseph P O'Shea et al.   NATURE METHODS

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

HMGB proteins: Interactions with DNA and chromatin

(2010) Michal Štros   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment

(2010) Stephen F. Altschul et al.   PLoS Computational Biology

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

Pseudocounts for transcription factor binding sites

(2008) Keishin Nishida et al.   NUCLEIC ACIDS RESEARCH

PSI-BLAST pseudocounts and the minimum description length principle

(2008) Stephen F. Altschul et al.   NUCLEIC ACIDS RESEARCH