FlaGs and webFlaGs : discovering novel biology through the analysis of gene neighbourhood conservation
(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
- Saha, Chayan Kumar LU ; Sanches Pires, Rodrigo ; Brolin, Harald ; Delannoy, Maxence and Atkinson, Gemma Catherine LU
- publishing date
- 2021
- 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
-
- scopus:85098455152
- pmid:32956448
- 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
- 2024-06-30 20:27:49
@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}}, }