TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure

Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequences can be homologous without sharing statistically significant amino acid or nucleotide identity, presenting a challenging bioinformatics problem. We present TreeDomViewer, a visualization tool available as a web-based interface that combines phylogenetic tree description, multiple sequence alignment and InterProScan data of sequences and generates a phylogenetic tree projecting the corresponding protein domain information onto the multiple sequence alignment. Thereby it makes use of existing domain prediction tools such as InterProScan. TreeDomViewer adopts an evolutionaryperspectiveonhowdomainstructureoftwoormore sequences can be aligned and compared, to subsequently infer the function of an unknown homolog. This provides insight into the function assignment of, in terms of amino acid substitution, very dive...

• Type: Journal
• Year: 2006
• Where: NAR
• Authors: Blaise T. F. Alako, Daphne Rainey, Harm Nijveen, Jack A. M. Leunissen
• Keywords: Multiple Sequence Alignment, NAR 2006, Phylogenetic Tree, Proteins