Sample data
Yersinia pestis KIM+                    Assembly level: Complete    FASTA format : Download     GenBank format : Download

Yersinia pestis strain NCTC5923  Assembly level: Contig         FASTA format : Download     GenBank format : Download

The genome file of Yersinia pestis KIM+ (NC_000418.fasta) is taken as an example to explain how to use Ori-Finder 2022 to predict replication origin in detail.
Upload the genome file
  • Users can upload a genome file with different assembly level in FASTA or GenBank format. If the uploaded file is in FASTA format, Ori-Finder will call Prodigal to predict gene locations. If the uploaded file is in GenBank format, Ori-Finder will obtain gene locations by parsing text.
tutorial
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The basic information about the genome
  • The principal indicator gene of Ori-Finder 2022 are dnaA by default and will be adjusted according to the lineage and chromosome type entered by users. Please refer to our article (Submitted) for details.
Program custom parameters
  • The default DnaA box motif is the standard motif (TTATCCACA) of E.coli, while the built-in DnaA box motif could be selected according to the organism or lineage of the uploaded genome. Because of the diversity of DnaA boxes, Ori-Finder 2022 also allows users to define their own DnaA box motifs.
Strand-biased analysis
  • Users can choose to perform strand-biased analysis on genomes assembled to the complete or chromosome level. Currently, Ori-Finder2022 does not support strand-biased analysis for genomes with scaffold or contig level.
  • If users only select strand-biased analysis without choosing or defining a dif motif, Ori-Finder will take the maximum of GC disparity as the replication terminus and perform strand-biased analysis.
  • If users choose or define a dif motif, Ori-Finder will combine the maximum of GC disparity and the dif motif to predict the replication terminus and perform strand-biased analysis. If there is no suitable dif site, Ori-Finder will still take the maximum of GC disparity as the replication terminus.