Paper Info
Title
GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs
Abstract
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.
Year
DOI
Venue
2021
10.1371/journal.pcbi.1009444
PLOS COMPUTATIONAL BIOLOGY
DocType
Volume
Issue
Journal
17
9
ISSN
Citations 
PageRank 
1553-734X
0
0.34
References 
Authors
0
5
Name
Order
Citations
PageRank
Manuel Tognon100.34
Vincenzo Bonnici2818.45
Erik Garrison3102.57
Rosalba Giugno481749.45
Luca Pinello5497.71