pseudoscan

Pseudo calling Criteria

Without exception, assign pseudo if either condition is met:

  • The isolate gene contains an internal stop or ends with a non-valid stop codon.

  • The isolate gene has an invalid reading frame (not divisible by three).

If the reference gene is pseudo, assign non-pseudo if both conditions are met:

  • The isolate gene does NOT have a reference-corresponding start or stop.

  • The reference gene has an invalid reading frame (not divisible by three).

Otherwise, assign pseudo

For all other genes, assign non-pseudo if either condition is met:

  • The isolate gene has a reference-corresponding start AND stop.

  • The isolate gene has a strong blastp match at the user specified thresholds.

Otherwise, assign pseudo

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note qualifiers added by pseudoscan

Each pseudo gene in the final annotation will contain a note field describing the primary reason it was assigned the pseudo tag. Also, some non-pseudo genes with interesting attributes will also contain notes describing why they are NOT marked pseudo, despite having a certain mutation. See below for special pseudo notes assigned and the specific conditions that trigger them:

Locus has a delayed stop codon

When a gene has a valid stop that extends beyond the last aligned base to the reference gene.

Locus has a valid alternative start site

When a gene has a valid start codon that does NOT correspond with the reference.

Locus has a valid alternative stop codon

When a gene has a valid stop codon that does NOT correspond with the reference.

Locus is (x) base pair(s) shorter than the reference

When a gene has a reference-corresponding start and stop, and the reference gene is shorter than the isolate gene.

Locus is (x) base pair(s) longer than the reference

When a gene has a reference-corresponding start and stop, and the reference gene is longer than the isolate gene.

Report Format

  • locus_tag: Locus tag of the annotated feature. In the hybran pipeline, pseudoscan is run before final locus tags have been determined, so the locus tags in those reports will still correspond to those assigned by RATT and the ab initio annotation.
  • gene_name: Assigned gene name (lifted over from reference annotation)
  • pseudo: Whether the feature has been called pseudo.
  • evidence_codes: Summary of the reason(s) for the pseudo determination. If multiple evidence codes apply to a single feature, they will be semicolon-delimited. See below for a description of the possible evidence codes.
  • summary: Semicolon-delimited string of (abbreviated) pseudo attributes and their respective boolean values.
  • div_by_3: Whether the feature sequence is divisible by three.
  • valid_start_codon: Whether the feature sequence begins with a valid start codon according to the detected genetic code table.
  • valid_stop_codon: Whether the feature sequence ends with a valid stop codon according to the detected genetic code table and has no internal stops.
  • ref_corr_start: Whether the feature sequence's beginning aligns to the reference sequence's beginning. Start refers to the part of the sequence containing the start codon, even for genes on the minus strand.
  • ref_corr_end: Whether the feature sequence's end aligns to the reference sequence's end. End here refers to the part of the sequence containing the stop codon, even for genes on the minus strand.
  • blast_ok: Whether the feature sequence has a passing blastp hit based on the thresholds configured with --seq-ident and --seq-covg.

Apart from locus_tag, gene_name, and evidence_codes, the column values are 0 (false), 1 (true), or . (not determined).

Evidence Codes

  • ref_pseudo: The reference gene is marked pseudo.
  • alt_start: The feature has a valid start codon that does NOT correspond with the reference.
  • alt_end: The feature has a valid stop codon that does NOT correspond with the reference.
  • noisy_seq: The feature has a reference-corresponding start and stop, but a poor blastp hit.
  • no_rcc: The feature does not have a reference-corresponding start and stop. The feature also has a poor blastp hit.
  • not_div_by_3: The feature does not have a valid reading frame.
  • internal_stop: The feature contains an internal stop codon.