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Regulatory proteins, such as Transcription Factors (TFs), are key genomic elements which promote or reduce the expression of genes by binding short, evolutionary conserved DNA sequences, often referred to as motifs. Mutations occurring in DNA motifs have been shown to have deleterious effects on the transcriptional landscape of the cell (Li & Ovcharenko, 2015; Guo et al., 2018). The recent introduction of Genome Variation Graphs (VG) (Garrison et al., 2018) allowed to represent in a single and efficient data-structure the genomic variation present within a population of individuals.
GRAFIMO (GRAph-based Finding of Individual Motif Occurrences) is a command-line tool that extends the traditional Position Weight Matrix (PWM) scanning procedure to VGs. GRAFIMO can search the occurrences of a given PWM in many genomes in a single run, accounting for the effects that SNPs, indels and potentially any structural variation (handled by VG) have on found potential motif occurrences. As result, GRAFIMO produces a report containing the statistically significant motif candidates found, reporting their frequency within the haplotypes embedded in the scanned VG and if they contain genomic variants or belong to the reference genome sequence.
- Required softwares and dependencies
- Install GRAFIMO via pip
- Install GRAFIMO via source code
- Install GRAFIMO via Bioconda
- Use GRAFIMO via Docker
- Single whole genome variation graph or a VG for each chromosome?
- Which file format for motifs?
- Searching motifs in genomes with a VG for each chromosome (suggested)
- Searching motifs in a single whole genome variation graph
- Command-line option
- How to build a genome VG with GRAFIMO