GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments

Sequence harmony: detecting functional specificity from alignments

Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. T...

ProtEST: protein multiple sequence alignments from expressed sequence tags

MOTIVATION An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs). ProtEST is more effective than a simple TBLASTN search of the query against the EST database, as the sequences are automatically clustered, assembled, made non-redundant, checked for sequence errors, ...

Chasing the ghost: recovering empty categories in the Chinese Treebank

Empty categories represent an important source of information in syntactic parses annotated in the generative linguistic tradition, but empty category recovery has only started to receive serious attention until very recently, after substantial progress in statistical parsing. This paper describes a unified framework in recovering empty categories in the Chinese Treebank. Our results show that ...

Prologue: Signal Transduction from an Historical Perspective

Tools for Fast Sequence Alignments