Background: With the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the mo...
Background: Sequence comparison faces new challenges today, with many complete genomes and large libraries of transcripts known. Gene annotation pipelines match these sequences in...
A challenging problem in bioinformatics is the detection of residues that account for protein function specificity, not only in order to gain deeper insight in the nature of functi...
Background: The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a sim...
— We describe a theoretical unifying framework to express comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supe...