Publications

Authors:

Tognon, Manuel; Bonnici, Vincenzo; Garrison, Erik; Giugno, Rosalba; Pinello, Luca

Title:

GRAFIMO: variant and haplotype aware motif scanning on pangenome graphs

Year:

2021

Type of item:

Articolo in Rivista

Tipologia ANVUR:

Articolo su rivista

Language:

Inglese

Referee:

No

Name of journal:

PLOS COMPUTATIONAL BIOLOGY

ISSN of journal:

1553-734X

N° Volume:

17

Number or Folder:

9

Page numbers:

1-10

Keyword:

Computational biology; Bioinformatics; Transcription Factor; Motif scanning; Genome graphs

Short description of contents:

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.

Web page:

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009444

Product ID:

122471

Handle IRIS:

11562/1049082

Last Modified:

November 14, 2024

Bibliographic citation:

Tognon, Manuel; Bonnici, Vincenzo; Garrison, Erik; Giugno, Rosalba; Pinello, Luca, GRAFIMO: variant and haplotype aware motif scanning on pangenome graphs «PLOS COMPUTATIONAL BIOLOGY» , vol. 17 , n. 9 , 2021 , pp. 1-10

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