Tutorial | DoriC 14.0: an updated database of prokaryotic replication origins with significantly expanded plasmid oriV annotations

1. Browse and filter records

Open Browse to search by name or accession, narrow the results with filters, and select an origin record to view its details.

One row represents one origin record. A chromosome or plasmid may have more than one record, so record counts are not counts of unique chromosomes or plasmids.

Quick search

Enter an Assembly ID, NC ID, Ori ID, organism name or plasmid description, then click Search. Try pSC101 or plasmid F.

If a name returns no results, clear active filters or try the accession. Some source descriptions omit familiar plasmid names; for R6K, use NZ_LT827129.1.

Advanced filters

Choose a genome type, organism group or other filters, then click Apply filters. To browse complete plasmids, select Complete and Plasmid. Use Reset all to remove filters.

Sort and scan

Click Genome size or GC content to sort the table. Use View to open a record.

Interpret literature linkage

Linked means a publication or source link is available; open References to read it. Not linked means no link is currently assigned. A link does not mean every predicted origin in the record was experimentally tested.

Quick search for pSC101 with its RefSeq accession and origin records — Search for **pSC101** and check accession `NC_002056.1` in the results.

Advanced Browse filters with Complete plasmids and highlighted evidence explanations — Select **Complete + Plasmid** to browse complete plasmid records.

2. Read a chromosome or plasmid record

Open a record to view its basic information, predicted origin location, reference links and sequence visualizations. Click an accession to open its NCBI entry.

References and reported locations

Click References to view the associated publications and available PubMed, DOI or full-text links.

Where available, the reported experimental region is listed separately from the predicted origin. It may describe a broader region; use the cited article and listed accession version when interpreting its coordinates. A dash means no location is supplied.

Origin and RIP information

Check the origin location, length and sequence composition. Replication initiation protein (RIP) information includes gene coordinates and protein features where available.

Organism identifies the source organism; Definition gives the original plasmid sequence description.

Origin visualization

Use the chromosome Z-curve and local oriC views, or the plasmid whole-sequence and oriV views, to inspect the origin and nearby features.

Available views

Views depend on the record type. Scaffold/Contig chromosome records show origin and Z-curve views, but do not include RIP protein or network panels.

Actual Scaffold chromosome record with assembly-aware detail panels — A Scaffold chromosome record with its available origin and Z-curve views.

Chromosome examples

Chromosome basic information and literature links — Check the chromosome accession, origin location and References in Basic information.

Chromosome Z-curve visualization — The interactive Z-curve module displays genome-wide nucleotide disparity profiles rotated at the maximum GC disparity. The plot integrates AT, GC, RY and MK disparity curves with replication-related annotations, including the identified replication origin, terminus, indicator genes, DnaA boxes and DnaA box clusters. This visualization provides a global compositional context for evaluating *oriC* localization and its consistency with replication-associated genomic signals.

Chromosome replication initiation protein information — The Replication Initiation Protein Information panel summarizes the initiation protein associated with the selected *oriC* entry. It reports gene coordinates, translated amino acid sequence and conserved-domain organization. These features provide protein context and should not be interpreted as direct experimental validation of the origin coordinates.

Chromosome oriC visualization — The *oriC* Visualization module provides an integrated view of the identified *oriC* region at both signal and sequence levels. The upper panel displays the transition probability profile across the candidate region, while the lower panel annotates replication-associated sequence features, including DnaA boxes, ATP-DnaA boxes, DnaA-trios, GATC sites, AT-rich regions and additional regulatory motifs. Flanking genes and motif orientations are also shown to support visual inspection of the local *oriC* architecture.

Archaeal chromosome origin visualization with ORB annotations — An archaeal *oriC* view with origin recognition box (ORB) annotations.

Plasmid examples

Plasmid Organism, Definition and Complete assembly category as separate fields — Check the plasmid accession, Organism and Definition in Basic information.

pRN1 reported experimental coordinates and associated publication — The pRN1 record links its reported region, `2101...5197 nt`, to PMID `25060695`.

Plasmid whole-sequence visualization — The Whole-sequence Visualization module provides a plasmid-scale view of sequence-composition and k-mer signals across the full plasmid sequence. GC disparity and k-mer cumulative scores are displayed together with the annotated RIP gene and *oriV* region, allowing users to evaluate the spatial relationship between replication-associated features and global sequence patterns. Interactive zooming enables detailed inspection of local regions while retaining whole-plasmid context.

Plasmid replication initiation protein information — The Replication Initiation Protein Information panel summarizes plasmid-encoded RIPs associated with the selected *oriV* record. It reports gene coordinates, strand orientation, translated amino acid sequence, MMseqs similarity hit, sequence identity, E-value and bitscore. Conserved-domain organization is displayed along the protein sequence to support comparative evaluation of the plasmid replication module.

Plasmid OriV visualization — The *oriV* Visualization module provides a detailed view of the identified plasmid replication origin. It displays the local GC profile and smoothed GC profile across the *oriV* region, highlights GC-rich and AT-rich segments, and annotates replication-associated cis-elements such as iterons and ColE-type sites. The genomic location, *oriV* type and evidence source are shown to facilitate visual assessment of plasmid replication origin annotations.

Plasmid genome visualization — The Plasmid Genome Visualization module provides an integrated circular and linear view of each plasmid sequence. The circular map summarizes plasmid-scale organization of coding and regulatory features, including RIP genes, annotated proteins, ncRNA or regulatory elements, *oriV* regions, iterons, DnaA boxes and BLAST-supported hits. The synchronized linear sequence view enables users to inspect local nucleotide sequences, translations, feature boundaries and strand orientations at base-level resolution.

3. Explore similar origins and RIP networks

Use comparative sequence support to explore similar origin sequences. Use RIP networks to explore sequence relationships among replication initiation protein subfamilies.

These categories describe sequence recurrence, not prediction confidence. They summarize how similar origin sequences are represented in the database. Literature links are shown separately.

Origin-sequence recurrence categories

Cross-taxon

At least five distinct nucleotide accessions and either at least three valid species or at least two valid genera contribute to the sequence cluster.

Multi-accession

At least three distinct nucleotide accessions contribute to the cluster, without meeting all Cross-taxon criteria.

Recurrent

At least two distinct nucleotide accessions, or at least two origin records, contribute to the cluster, without meeting the higher categories.

Singleton

One origin record occurs in the sequence group. This does not mean the origin is biologically new.

Record groups

Comparisons are made separately for bacterial and archaeal chromosomes and plasmids. Scaffold/Contig chromosome records are marked Not analyzed.

Top 10 similar origins

Open a related Ori ID to view its record. Compare sequence identity and reciprocal coverage in the table; related records need not belong to the same sequence group.

RIP sequence-similarity networks

Choose one of the four tabs on the Home page and click Open full view. Search by accession or Ori ID, then select a node to view its protein subfamily and annotations. Edges show sequence similarity, not protein interactions.

Optional: sequence comparison settings

Sequence groups use 80% nucleotide identity and 80% reciprocal coverage. Related-origin links use 70% identity and 50% reciprocal coverage for broader browsing. These empirical settings are not prediction-confidence thresholds.

Current DoriC 14.0 comparative sequence support summary and related origins — Check the sequence-recurrence category and use the related-origins table to open similar records.

Current DoriC 14.0 RIP sequence-similarity networks overview — Switch between the four RIP networks and search for an accession or Ori ID.

Archaeal plasmid RIP network with a selected subfamily and Pfam domains — Select a node to view its representative protein and domain annotations.

4. Search with BLAST

Open Search, choose a database, paste or upload a nucleotide FASTA sequence, and click Submit BLAST.

Submit a query

Paste FASTA text or upload a plain-text FASTA file. To try the search, click Load example FASTA. The example includes bacterial and archaeal chromosomes and plasmids.

You can submit up to 20 sequences and 10,000,000 bases in total; file uploads must be no larger than 10 MB. Give each FASTA record a unique name after >.

Read the results

Results are grouped by your submitted sequence. Use the hit-position plot and table to compare matches, their locations, identity and coverage.

Open the matching record

Click a DoriC Ori ID to open its record. Manually compiled targets show source names and available NCBI or publication links.

View and save results

Wait for the results page, then download the TSV to save your matches. Results are available for approximately 24 hours in the same browser session. Click New search to start again. If a service error appears, retry later; it does not mean no match was found.

Choose a search database

DoriC 14.0 origin sequences searches predicted origins from plasmids and complete/chromosome records. Scaffold/Contig records are available in Browse and downloads, but not in this search database.

Manually compiled origin sequences searches a separate collection of origin-associated sequences, including examples without a RefSeq record. Some sequences include flanking or broader replication regions. A sequence match alone does not confirm origin activity.

Start with the default settings for your chosen database. Open Advanced options to change the search settings. Maximum target sequences limits database targets per query, not alignment rows. Changing databases restores its defaults. The results page shows the settings used.

The plot and table initially show alignments covering at least 50% of the target sequence. Use the coverage selector to change this or choose All to include partial matches. A display filter changes which matches you see, not the search itself.

Understand the result fields

Result field	Meaning
Bit score / E-value	Results list smaller E-values first, then larger bit scores. These describe the alignment, not origin confidence.
Per. identity	Percentage of identical positions within the local alignment, not across the whole uploaded plasmid.
Query coverage	Percentage of your uploaded sequence spanned by this alignment. A short origin match may cover only a small part of a whole chromosome or plasmid, even with high identity.
Origin / Target coverage	Percentage of the database sequence spanned by this alignment. The label is Origin coverage for DoriC and Target coverage for the manually compiled collection.
Query hit position (bp)	Start and end positions of the alignment in your uploaded sequence.
Subject range (bp)	Start and end positions in the database sequence. Plus/minus indicates alignment orientation, not replication direction.

Use Full query to see where matches fall along your entire sequence, or Hit region to zoom in. The blue track shows query GC content. Hover over a hit for details, or click it to find the corresponding table row.

Each row is one local alignment, also called an HSP. Download all HSPs (TSV) saves all reported alignments, including those hidden by the display filter. If no hits pass the filter, try All before concluding there are no reported matches.

Current BLAST form with the ordered chromosome and plasmid example and advanced options — Choose a database, load the example or upload FASTA, and click Submit BLAST.

Full query shows match positions across the entire uploaded sequence and its GC content.

Hit-region zoom of the same BLAST matches and existing GC windows — Hit region zooms to the displayed matches without changing the alignment results.

Per-HSP BLAST results with target coverage and uploaded query coordinates — Compare identity, coverage and hit positions in the table. Choose All to show partial matches.

Actual saved BLAST parameters on the results page — Check the search settings used for these results.

5. Download data

Open Download to get a complete release, export records matching your filters, or select individual records to save.

One CSV row represents one origin record. Reported experimental coordinates and predicted origin coordinates are listed separately.

Download packaged releases

Choose a DoriC release to download its package. The manually compiled sequence collection is available separately.

Filter DoriC 14.0 records

Set your filters and apply them to preview the matching records.

Download filtered CSV

Use the filtered CSV download to save all records matching your filters, not just the current page.

Download selected CSV

Select one or more rows in the preview table, then download only those records.

Packaged releases and three downloads for manually compiled origin-associated sequences — Download a DoriC release or the separate manually compiled sequence collection.

Filtered download form with Complete plasmids and taxonomy filters — Apply filters to choose which records are included in the CSV download.

Preview with two Complete plasmid rows selected for CSV download — Select records in the preview, then download the selected CSV. Use Clear selection to start over.

DoriC 14.0 tutorial