Viral Genome Notation Parser

Parse canonical viral genome notation and derive Baltimore class; not a species identifier.

Description

Parse canonical DNA or RNA genome notation into molecule, strand count, sense, reverse-transcription status, and Baltimore class.

Viral genome notation combines several properties. DNA and RNA identify the genetic molecule; ss and ds mean single-stranded and double-stranded. For single-stranded RNA, a plus sign denotes positive sense and a minus sign denotes negative sense relative to messenger RNA. Positive-sense RNA can serve as messenger RNA, whereas negative-sense RNA requires a complementary transcript.^[1]

The Baltimore classification organizes viruses into seven groups according to genome type and the route used to produce messenger RNA. Reverse-transcribing groups use a DNA or RNA intermediate and are distinguished from otherwise similar genome types. This classification summarizes replication strategy and is separate from a taxonomic species or lineage assignment.

Viral Genome Notation Parser reads a compact, case-sensitive notation such as ssRNA+ or dsDNA-RT. It returns the encoded properties and the corresponding Roman-numeral class. It parses the supplied label rather than inspecting a nucleotide sequence.

When to interpret a viral genome label

Use the parser to turn a canonical genome label into structured fields for teaching notes, tables, or metadata checks. It can also expose missing qualifiers, such as ssRNA without a required sense sign.

Map canonical genome notation to Baltimore classes I through VII.
Check whether sense and reverse-transcription qualifiers form an accepted combination.
Separate a genome-type label from a lineage name or species identifier.

How to enter genome notation and derive its class

Enter ss or ds immediately followed by uppercase DNA or RNA.
For ordinary single-stranded RNA, append + or -. Append -RT for a supported reverse-transcribing genome.
Run the parser and read molecule, strandedness, sense, reverse transcribing, and Baltimore class.
If input is rejected, check letter case, internal spaces, qualifier order, and the accepted combinations below.

The implementation trims whitespace at the beginning and end, then matches the pattern ^(ss|ds)(DNA|RNA)([+-])?(-RT)?$. It does not change case or remove internal whitespace. After matching, it rejects sense signs on DNA or double-stranded genomes, ordinary ssRNA without a sense sign, and incompatible reverse-transcription qualifiers.

Accepted notation	Baltimore class	Returned sense
dsDNA	I	unspecified
ssDNA	II	unspecified
dsRNA	III	unspecified
ssRNA+	IV	positive
ssRNA-	V	negative
ssRNA-RT or ssRNA+-RT	VI	unspecified or positive, respectively
dsDNA-RT	VII	unspecified

Reverse-transcribing RNA must be single-stranded and cannot have negative sense; reverse-transcribing DNA must be double-stranded. In accepted reverse-transcribing inputs, -RT selects class VI for RNA or VII for DNA. Otherwise molecule, strandedness, and RNA sense select classes I through V.

json

{
  "input": {
    "notation": "ssRNA+"
  },
  "output": {
    "molecule": "RNA",
    "strandedness": "single",
    "sense": "positive",
    "reverseTranscribing": false,
    "baltimoreClass": "IV"
  }
}

json

{
  "input": {
    "notation": "dsDNA-RT"
  },
  "output": {
    "molecule": "DNA",
    "strandedness": "double",
    "sense": "unspecified",
    "reverseTranscribing": true,
    "baltimoreClass": "VII"
  }
}

Limitations of canonical notation parsing

Only the listed syntax is accepted. Forms such as (+)ssRNA, ds DNA, lowercase rna, or ambisense labels are not normalized into it.
The parser does not identify a species, verify that a label matches a real genome, query a taxonomy database, or inspect sequence data.
Segmentation, circularity, genome length, and additional replication features are not represented.

For ssRNA-RT, the returned sense is unspecified because the notation contains no sense sign. This is a property of the input string; it should not be read as a biological assertion that class VI lacks a defined replication strategy.

Alternative or Complementary genome metadata checks

Use curated taxonomy and sequence annotation when the question concerns organism identity or observed genome structure. A lineage format audit checks a different label syntax, while a segment-combination calculation answers a separate question about possible parental segment sources.

References

The Baltimore Classification of Viruses 50 Years Later: How Does It Stand in the Light of Virus Evolution? — Microbiology and Molecular Biology Reviews / American Society for Microbiology

Similar or alternative tools

Lineage Format Audit
Check a lineage label against its supplied numeric-depth limit; format validity does not assign taxonomy.
Segment Reassortment Combinations
Count theoretical segment-source combinations from supplied segment and parental-strain counts.