GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
09 2021
09 2021
Historique:
received:
11
01
2021
accepted:
10
09
2021
revised:
15
10
2021
pubmed:
28
9
2021
medline:
27
11
2021
entrez:
27
9
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34570769
doi: 10.1371/journal.pcbi.1009444
pii: PCOMPBIOL-D-21-00041
pmc: PMC8519448
doi:
Substances chimiques
Transcription Factors
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1009444Subventions
Organisme : NHGRI NIH HHS
ID : R00 HG008399
Pays : United States
Organisme : NHGRI NIH HHS
ID : R35 HG010717
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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