Taxonomic colouring of phylogenetic trees of protein sequences

Publikationstyp:

Zeitschriftenaufsatz

Metadaten:

Autoren

G Palidwor
EG Reynaud
MA Andrade-Navarro

Autoren-URL

https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000235702200001&DestLinkType=FullRecord&DestApp=WOS_CPL

DOI

10.1186/1471-2105-7-79

Externe Identifier

Clarivate Analytics Document Solution ID: 017OF
PubMed Identifier: 16503967

ISSN

1471-2105

Zeitschrift

BMC BIOINFORMATICS

Artikelnummer

ARTN 79

Datum der Veröffentlichung

2006

Status

Published

Titel

Taxonomic colouring of phylogenetic trees of protein sequences

Sub types

Article

Ausgabe der Zeitschrift

Datenquelle: Web of Science (Lite)

Andere Metadatenquellen:

Abstract

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.ogic.ca/projects/phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address.

Autoren

Gareth Palidwor
Emmanuel G Reynaud
Miguel A Andrade-Navarro

DOI

10.1186/1471-2105-7-79

eISSN

1471-2105

Ausgabe der Veröffentlichung

Zeitschrift

BMC Bioinformatics

Sprache

Artikelnummer

Online publication date

2006

Datum der Veröffentlichung

2006

Status

Published

Herausgeber

Springer Science and Business Media LLC

Herausgeber URL

http://dx.doi.org/10.1186/1471-2105-7-79

Datum der Datenerfassung

2021

Titel

Taxonomic colouring of phylogenetic trees of protein sequences

Ausgabe der Zeitschrift

Datenquelle: Crossref

Abstract

<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusion</h4>PhyloView can be used at http://www.ogic.ca/projects/phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address.

Addresses

Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth, Ottawa, ON K1H 8L6, Canada. gpalidwor@ohri.ca

Autoren

Gareth Palidwor
Emmanuel G Reynaud
Miguel A Andrade-Navarro

DOI

10.1186/1471-2105-7-79

eISSN

1471-2105

Externe Identifier

PubMed Identifier: 16503967
PubMed Central ID: PMC1386715

Open access

true

ISSN

1471-2105

Zeitschrift

BMC bioinformatics

Schlüsselwörter

Proteome
Sequence Analysis, Protein
Evolution, Molecular
Phylogeny
Amino Acid Sequence
Algorithms
Color
Software
User-Computer Interface
Molecular Sequence Data

Sprache

eng

Medium

Electronic

Online publication date

2006

Open access status

Open Access

Paginierung

Datum der Veröffentlichung

2006

Status

Published

Publisher licence

CC BY

Datum der Datenerfassung

2006

Titel

Taxonomic colouring of phylogenetic trees of protein sequences.

Sub types

product-review
Research Support, Non-U.S. Gov't
Journal Article

Ausgabe der Zeitschrift

Files

https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-79 https://europepmc.org/articles/PMC1386715?pdf=render

Datenquelle: Europe PubMed Central

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.ogic.ca/projects/phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address.

Date of acceptance

2006

Autoren

Gareth Palidwor
Emmanuel G Reynaud
Miguel A Andrade-Navarro

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/16503967

DOI

10.1186/1471-2105-7-79

eISSN

1471-2105

Externe Identifier

PubMed Central ID: PMC1386715

Zeitschrift

BMC Bioinformatics

Schlüsselwörter

Algorithms
Amino Acid Sequence
Color
Evolution, Molecular
Molecular Sequence Data
Phylogeny
Proteome
Sequence Analysis, Protein
Software
User-Computer Interface

Sprache

eng

Country

England

Paginierung

PII

1471-2105-7-79

Datum der Veröffentlichung

2006

Status

Published online

Datum, an dem der Datensatz öffentlich gemacht wurde

2006

Titel

Taxonomic colouring of phylogenetic trees of protein sequences.

Sub types

Journal Article
Research Support, Non-U.S. Gov't

Ausgabe der Zeitschrift

Datenquelle: PubMed

Beziehungen:

Eigentum von

Bioinformatik

Taxonomic colouring of phylogenetic trees of protein sequences

Files

Werkzeuge