Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated muta...

A new Markovian method for the prediction of phylogenetic trees has been developed earlier by the authors. Here, the method is illustrated and applied using mitochondrial DNA data for vertebrate species (and technicalities of the theory are avoided). Discussions include the sensitivity of the results to DNA alignment techniques and the inclusion of polytomy in tree structures. Several compariso...

A new Markovian method for the prediction of phylogenetic trees has been developed earlier by the authors. Here, the method is illustrated and applied using mitochondrial DNA data for vertebrate species (and technicalities of the theory are avoided). Discussions include the sensitivity of the results to DNA alignment techniques and the inclusion of polytomy in tree structures. Several compariso...

Why align sequences? Sequence alignments can reveal many things about the functional, structural or evolutionary significance of regions of DNA, RNA or protein. Examples: • The degree of similarity between regions of amino acids can tell us how well that region is conserved, which can provide clues about the structural or functional significance of that region. • The DNA sequence alignment of m...

A test that can detect the influence of differential lineage sorting on phylogenetic signal in integrated studies with two or more loci is presented. Hitherto unexplored consequences of relationships among gene trees and species trees are made explicit, revealing potential influences of differential lineage sorting on phylogenetic signal. These influences can result in observable consequences, ...

The phylogenetic relationships among members of the Odonates were inferred from mitochondrial DNA 12S ribosomal RNA sequence data. These data show support for a monophyletic Anisoptera suborder, which are consistent with previous phylogenetic work performed on the group. However, the Zygoptera are paraphyletic based on mitochondrial DNA evidence. In particular, the family Lestidae appears more ...

In this paper it is introduced a new methodology for the analysis of barcode sequences. Barcode DNA is a very short nucleotide sequence, corresponding for the animal kingdom to the mitochondrial gene cytochrome c oxidase subunit 1, that acts as a unique element for identification and taxonomic purposes. Traditional barcode analysis uses well consolidated bioinformatics techniques such as sequen...

Aphid soldiers, altruistic larvae that protect the colony from predators, are an example of highly social behaviour in an insect group with a natural history different from the eusocial Hymenoptera and Isoptera. Aphids therefore allow independent tests of theory developed to explain the evolution of eusociality. Although soldiers have been discovered in five tribes from two families, the number...

MOTIVATION Phylogenetic profiling methods can achieve good accuracy in predicting protein-protein interactions, especially in prokaryotes. Recent studies have shown that the choice of reference taxa (RT) is critical for accurate prediction, but with more than 2500 fully sequenced taxa publicly available, identifying the most-informative RT is becoming increasingly difficult. Previous studies on...