An assessment of substitution scores for protein profile–profile comparison

A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

(2011) Dapeng Zhang et al.   NUCLEIC ACIDS RESEARCH

Identification of novel families and classification of the C2 domain superfamily elucidate the origin and evolution of membrane targeting activities in eukaryotes

(2010) Dapeng Zhang et al.   GENE

Quality measures for protein alignment benchmarks

(2010) Robert C. Edgar   NUCLEIC ACIDS RESEARCH

Comparison of sequence profiles. Strategies for structural predictions using sequence information

(2010) Leszek Rychlewski et al.   PROTEIN SCIENCE

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

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

PSI-BLAST pseudocounts and the minimum description length principle

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