GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.

Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference ge...

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Autores principales:	Manuel Tognon, Vincenzo Bonnici, Erik Garrison, Rosalba Giugno, Luca Pinello
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/a139b8b3383047a48810a794b90b50ba
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spelling	oai:doaj.org-article:a139b8b3383047a48810a794b90b50ba2021-12-02T19:58:13ZGRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.1553-734X1553-735810.1371/journal.pcbi.1009444https://doaj.org/article/a139b8b3383047a48810a794b90b50ba2021-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009444https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference genomes, no tool exists to find them in pangenome variation graphs (VGs). VGs are sequence-labelled graphs that can efficiently encode collections of genomes and their variants in a single, compact data structure. Because VGs can losslessly compress large pangenomes, TFBS scanning in VGs can efficiently capture how genomic variation affects the potential binding landscape of TFs in a population of individuals. Here we present GRAFIMO (GRAph-based Finding of Individual Motif Occurrences), a command-line tool for the scanning of known TF DNA motifs represented as Position Weight Matrices (PWMs) in VGs. GRAFIMO extends the standard PWM scanning procedure by considering variations and alternative haplotypes encoded in a VG. Using GRAFIMO on a VG based on individuals from the 1000 Genomes project we recover several potential binding sites that are enhanced, weakened or missed when scanning only the reference genome, and which could constitute individual-specific binding events. GRAFIMO is available as an open-source tool, under the MIT license, at https://github.com/pinellolab/GRAFIMO and https://github.com/InfOmics/GRAFIMO.Manuel TognonVincenzo BonniciErik GarrisonRosalba GiugnoLuca PinelloPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 9, p e1009444 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Manuel Tognon Vincenzo Bonnici Erik Garrison Rosalba Giugno Luca Pinello GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
description	Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference genomes, no tool exists to find them in pangenome variation graphs (VGs). VGs are sequence-labelled graphs that can efficiently encode collections of genomes and their variants in a single, compact data structure. Because VGs can losslessly compress large pangenomes, TFBS scanning in VGs can efficiently capture how genomic variation affects the potential binding landscape of TFs in a population of individuals. Here we present GRAFIMO (GRAph-based Finding of Individual Motif Occurrences), a command-line tool for the scanning of known TF DNA motifs represented as Position Weight Matrices (PWMs) in VGs. GRAFIMO extends the standard PWM scanning procedure by considering variations and alternative haplotypes encoded in a VG. Using GRAFIMO on a VG based on individuals from the 1000 Genomes project we recover several potential binding sites that are enhanced, weakened or missed when scanning only the reference genome, and which could constitute individual-specific binding events. GRAFIMO is available as an open-source tool, under the MIT license, at https://github.com/pinellolab/GRAFIMO and https://github.com/InfOmics/GRAFIMO.
format	article
author	Manuel Tognon Vincenzo Bonnici Erik Garrison Rosalba Giugno Luca Pinello
author_facet	Manuel Tognon Vincenzo Bonnici Erik Garrison Rosalba Giugno Luca Pinello
author_sort	Manuel Tognon
title	GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
title_short	GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
title_full	GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
title_fullStr	GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
title_full_unstemmed	GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
title_sort	grafimo: variant and haplotype aware motif scanning on pangenome graphs.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/a139b8b3383047a48810a794b90b50ba
work_keys_str_mv	AT manueltognon grafimovariantandhaplotypeawaremotifscanningonpangenomegraphs AT vincenzobonnici grafimovariantandhaplotypeawaremotifscanningonpangenomegraphs AT erikgarrison grafimovariantandhaplotypeawaremotifscanningonpangenomegraphs AT rosalbagiugno grafimovariantandhaplotypeawaremotifscanningonpangenomegraphs AT lucapinello grafimovariantandhaplotypeawaremotifscanningonpangenomegraphs
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GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.

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