FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation

Chayan Kumar Saha; Rodrigo Sanches Pires; Harald Brolin; Maxence Delannoy; Gemma Catherine Atkinson

doi:10.1093/bioinformatics/btaa788

FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation

Chayan Kumar Saha, Rodrigo Sanches Pires, Harald Brolin, Maxence Delannoy, Gemma Catherine Atkinson

Umeå University

Research output: Contribution to journal › Article › peer-review

Abstract

SUMMARY: Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin-antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run.

AVAILABILITY AND IMPLEMENTATION: FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	1312-1314
Journal	Bioinformatics
Volume	37
Issue number	9
DOIs	https://doi.org/10.1093/bioinformatics/btaa788
Publication status	Published - 2021
Externally published	Yes

Free keywords

Biology
Emblems and Insignia
Evolution, Molecular
Phylogeny
Software

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Cite this

@article{b066631b2a81425e93bf366fdb9e16fe,

title = "FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation",

abstract = "SUMMARY: Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin-antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run.AVAILABILITY AND IMPLEMENTATION: FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",

keywords = "Biology, Emblems and Insignia, Evolution, Molecular, Phylogeny, Software",

author = "Saha, {Chayan Kumar} and {Sanches Pires}, Rodrigo and Harald Brolin and Maxence Delannoy and Atkinson, {Gemma Catherine}",

note = "{\textcopyright} The Author(s) 2020. Published by Oxford University Press.",

year = "2021",

doi = "10.1093/bioinformatics/btaa788",

language = "English",

volume = "37",

pages = "1312--1314",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

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TY - JOUR

T1 - FlaGs and webFlaGs

T2 - discovering novel biology through the analysis of gene neighbourhood conservation

AU - Saha, Chayan Kumar

AU - Sanches Pires, Rodrigo

AU - Brolin, Harald

AU - Delannoy, Maxence

AU - Atkinson, Gemma Catherine

N1 - © The Author(s) 2020. Published by Oxford University Press.

PY - 2021

Y1 - 2021

N2 - SUMMARY: Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin-antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run.AVAILABILITY AND IMPLEMENTATION: FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - SUMMARY: Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin-antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run.AVAILABILITY AND IMPLEMENTATION: FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

KW - Biology

KW - Emblems and Insignia

KW - Evolution, Molecular

KW - Phylogeny

KW - Software

U2 - 10.1093/bioinformatics/btaa788

DO - 10.1093/bioinformatics/btaa788

M3 - Article

C2 - 32956448

SN - 1367-4803

VL - 37

SP - 1312

EP - 1314

JO - Bioinformatics

JF - Bioinformatics

IS - 9

ER -

FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation

Abstract

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