BioLayout--an Automatic Graph Layout Algorithm for Similarity Visualization

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2001 Oct 9

PMID 11590107

Citations 48

Authors

A J Enright

C A Ouzounis

Affiliations

Soon will be listed here.

Abstract

Unlabelled: Graph layout is extensively used in the field of mathematics and computer science, however these ideas and methods have not been extended in a general fashion to the construction of graphs for biological data. To this end, we have implemented a version of the Fruchterman Rheingold graph layout algorithm, extensively modified for the purpose of similarity analysis in biology. This algorithm rapidly and effectively generates clear two (2D) or three-dimensional (3D) graphs representing similarity relationships such as protein sequence similarity. The implementation of the algorithm is general and applicable to most types of similarity information for biological data.

Availability: BioLayout is available for most UNIX platforms at the following web-site: http://www.ebi.ac.uk/research/cgg/services/layout.

Citing Articles

Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure.

Lisowski P, Lickfett S, Rybak-Wolf A, Menacho C, Le S, Pentimalli T Nat Commun. 2024; 15(1):7027.

PMID: 39174523 PMC: 11341898. DOI: 10.1038/s41467-024-51216-w.

CGG toolkit: Software components for computational genomics.

Vasileiou D, Karapiperis C, Baltsavia I, Chasapi A, Ahren D, Janssen P PLoS Comput Biol. 2023; 19(11):e1011498.

PMID: 37934729 PMC: 10629618. DOI: 10.1371/journal.pcbi.1011498.

DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.

Weng Z, Yue Z, Zhu Y, Chen J Bioinformatics. 2022; 38(Suppl 1):i359-i368.

PMID: 35758816 PMC: 9235497. DOI: 10.1093/bioinformatics/btac261.

Protein-protein interactions: Methods, databases, and applications in virus-host study.

Farooq Q, Shaukat Z, Aiman S, Li C World J Virol. 2021; 10(6):288-300.

PMID: 34909403 PMC: 8641042. DOI: 10.5501/wjv.v10.i6.288.

Identifying Neuropeptide and G Protein-Coupled Receptors of Juvenile Oriental River Prawn () in Response to Salinity Acclimation.

Sun S, Zhu M, Pan F, Feng J, Li J Front Endocrinol (Lausanne). 2020; 11:623.

PMID: 33013701 PMC: 7506046. DOI: 10.3389/fendo.2020.00623.