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The alignment of protein superfamily sequences Part I: Identifying Cluster Specific Subsequences (CSS) in Protein Families
Multiple Sequence Alignments (MSA) are crucial tools in protein bioinformatics. Despite recent advances such as obtained by MAFFT and Promals3D, MSA construction of complex superfamilies remains problematic and requires ...
Positive Selection is shaping the Evolution of two Aspartic Proteinases in phytopathogenic Botrytis species
A significantly higher nonsynonymous (dN) than synonymous (dS) substitution rate is a powerful landmark of positive Darwinian selection . The rate ratio ω=dN/dS measures the magnitude and direction of selective pressure ...
The alignment of protein superfamily sequences Part II: Multiple Alignment Touch-up Engine (MATE)
Multiple Sequence Alignments (MSA) are crucial tools in protein bioinformatics. Despite recent advances, construction of MSAs for complex superfamilies remains problematic and requires rigorous manual correction. In this ...
Evolution and Structure-Function Prediction of Eqolisins in Fungi
Botrytis cinerea is a phytopathogenic fungus that acidifies its environment (pH<4), which has been shown to be related with the spectrum of secreted hydrolytic enzymes that are involved in the degradation of the host's ...
HMMer CTTer: Function assignation using HMMer profiles and reliable cut-offs