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4.9.3 SeRP properties

serp_properties

serp_properties calculates codon-usage statistics and translated-protein properties from nucleotide FASTA sequences.

Function

Use this command when you want to:

  • summarize codon frequency for each sequence;
  • calculate RSCU and CAI-like codon-usage tables;
  • summarize whole-input codon usage;
  • translate nucleotide sequences and calculate protein properties such as GRAVY, flexibility, instability index, isoelectric point, and secondary-structure fractions.

Although this page is placed under SeRP analysis, the command is sequence based. It does not read a SeRP peak table directly.

Input

The input should be a nucleotide FASTA file containing coding sequences.

Requirements:

  • each sequence length should be a multiple of 3;
  • sequences are translated in the current reading frame;
  • a terminal stop codon is removed before protein-property calculation;
  • sequences containing internal stop codons are skipped during protein-property output.

Parameters

Parameter Required Meaning
-f yes Input nucleotide FASTA file.
-o yes Output prefix.

Output

Output Description
<prefix>_frequency.txt Per-sequence codon frequency table.
<prefix>_rscu.txt Per-sequence RSCU table.
<prefix>_cai.txt Per-sequence CAI-like codon usage table.
<prefix>_whole_codon_usage.txt Whole-input codon usage summary.
<prefix>.Properties.txt Translated-protein property table.

The protein property table contains:

Column Description
ID FASTA record ID.
Seq Translated amino-acid sequence.
Length Amino-acid sequence length after removing a terminal stop codon, if present.
Gravy Grand average of hydropathy.
Flexibility Average predicted flexibility.
Instability Instability index.
Isoelectric_Point Predicted isoelectric point.
Helix Predicted helix fraction.
Turn Predicted turn fraction.
Sheet Predicted sheet fraction.

Examples

Calculate sequence properties for CDS sequences:

serp_properties \
  -f CDS_sequences.fa \
  -o CDS_properties

Calculate properties for peak-associated sequences retrieved from a FASTA file:

serp_properties \
  -f SeRP_peak_sequences.fa \
  -o SeRP_peak_properties

Notes

  • The command expects nucleotide sequences, not amino-acid FASTA input.
  • Sequence lengths that are not divisible by 3 will raise an error during codon counting.
  • Internal stop codons cause the affected sequence to be skipped in the protein-property table.
  • The generated <prefix>.Properties.txt uses a dot before Properties, while the codon-usage outputs use underscores.