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

Saha, Chayan Kumar LU orcid ; Sanches Pires, Rodrigo ; Brolin, Harald ; Delannoy, Maxence and Atkinson, Gemma Catherine LU (2021) In Bioinformatics 37(9). p.1312-1314
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... (More)

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.

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author
; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Biology, Emblems and Insignia, Evolution, Molecular, Phylogeny, Software
in
Bioinformatics
volume
37
issue
9
pages
1312 - 1314
publisher
Oxford University Press
external identifiers
  • pmid:32956448
  • scopus:85098455152
ISSN
1367-4803
DOI
10.1093/bioinformatics/btaa788
language
English
LU publication?
no
id
b066631b-2a81-425e-93bf-366fdb9e16fe
date added to LUP
2021-09-27 15:51:11
date last changed
2024-04-20 12:58:03
@article{b066631b-2a81-425e-93bf-366fdb9e16fe,
  abstract     = {{<p>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.</p><p>AVAILABILITY AND IMPLEMENTATION: FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/.</p><p>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.</p>}},
  author       = {{Saha, Chayan Kumar and Sanches Pires, Rodrigo and Brolin, Harald and Delannoy, Maxence and Atkinson, Gemma Catherine}},
  issn         = {{1367-4803}},
  keywords     = {{Biology; Emblems and Insignia; Evolution, Molecular; Phylogeny; Software}},
  language     = {{eng}},
  number       = {{9}},
  pages        = {{1312--1314}},
  publisher    = {{Oxford University Press}},
  series       = {{Bioinformatics}},
  title        = {{FlaGs and webFlaGs : discovering novel biology through the analysis of gene neighbourhood conservation}},
  url          = {{http://dx.doi.org/10.1093/bioinformatics/btaa788}},
  doi          = {{10.1093/bioinformatics/btaa788}},
  volume       = {{37}},
  year         = {{2021}},
}