Background: The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. How...
Protein sequence alignments are more reliable the shorter the evolutionary distance. Here, we align distantly related proteins using many closely spaced intermediate sequences as ...
A complete understanding of transcriptional regulatory processes in the cell requires identification of transcription factor binding sites on a genomewide scale. Unfortunately, th...
In this paper we investigate the general problem of discovering recurrent patterns that are embedded in categorical sequences. An important real-world problem of this nature is mo...
Background: The pyridine nucleotide disulfide reductase (PNDR) is a large and heterogeneous protein family divided into two classes (I and II), which reflect the divergent evoluti...