Taxonomic colouring of phylogenetic trees of protein sequences

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Title: Taxonomic colouring of phylogenetic trees of protein sequences
Authors: Palidwor, GarethReynaud, Emmanuel G.Andrade, Miguel A.
Permanent link: http://hdl.handle.net/10197/11789
Date: 17-Feb-2006
Online since: 2020-12-08T12:35:28Z
Abstract: Background: Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common. Results: We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree. Conclusion: PhyloView can be used at http:/www.og ic.ca/projects/ phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address. © 2006 Palidwor et al; licensee BioMed Central Ltd.
Funding Details: Canadian Foundation for Innovation, and the Ontario Research and Development Challenge Funds
Type of material: Journal Article
Publisher: Springer
Journal: BMC Bioinformatics
Volume: 7
Copyright (published version): 2006 the Authors
Keywords: ProteomeProtein sequence analysisPhylogenyAmino acid sequenceAlgorithmsUser-computer interfaceMolecular sequence data
DOI: 10.1186/1471-2105-7-79
Language: en
Status of Item: Peer reviewed
ISSN: 1471-2105
This item is made available under a Creative Commons License: https://creativecommons.org/licenses/by-nc-nd/3.0/ie/
Appears in Collections:Biomolecular and Biomedical Science Research Collection

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