4.8.1 smORF scanner¶

Function¶

smorf_scanner scans transcript-centric candidate ORFs from a genome FASTA file and a genePred annotation file.

It reconstructs spliced transcript sequences, searches candidate ORFs using user-defined start codons and ORF length limits, classifies ORF categories, optionally marks overlapping/nested ORFs, and writes ORF annotation and sequence files.

Input files¶

Input	Required	Description
Genome FASTA	Yes	Genome sequence used to reconstruct transcript sequences.
genePred annotation	Yes	Transcript annotation in genePred format.

Parameters¶

Parameter	Required	Description
`-g`, `--genome`	Yes	Input genome FASTA file.
`-a`, `--annotation`	Yes	Input transcript annotation in genePred format.
`-o`, `--out-prefix`	No	Prefix of output files. Default: `ORF`.
`-p`, `--orf-prefix`	No	Prefix used to generate stable ORF IDs. Default: `ORF`.
`-s`, `--start-codons`	No	Comma-separated start codons used for ORF scanning. Default: `ATG`.
`-m`, `--min-aa`	No	Minimum ORF peptide length in amino acids. Default: `8`.
`-M`, `--max-aa`	No	Maximum ORF peptide length in amino acids. Default: `10000`.
`-x`, `--scan-strand`	No	Strand mode for scanning: `sense`, `antisense`, or `both`. Default: `sense`.
`-u`, `--kozak-up`	No	Number of upstream nucleotides extracted for Kozak context. Default: `6`.
`-d`, `--kozak-down`	No	Number of downstream nucleotides after the start codon extracted for Kozak context. Default: `6`.
`-t`, `--threads`	No	Number of worker processes used for ORF scanning. Default: `1`.
`-O`, `--mark-overlap`	No	Mark nested or overlapping ORFs after scanning. Default: `False`.
`-R`, `--remove-discarded`	No	Remove same-frame internal ORFs marked as discarded. Default: `False`.
`-I`, `--include-stop`	No	Keep the stop-codon symbol in peptide sequences. Default: `False`.

Output files¶

Assuming -o smorf.raw, the command writes:

Output	Description
`smorf.raw.genePred`	ORF annotation in a genePredExt-like format.
`smorf.raw.message.txt`	Full ORF information table. This is the main input for `smorf_filter`.
`smorf.raw.nt.fa`	Candidate ORF nucleotide sequences in FASTA format.
`smorf.raw.pep.fa`	Candidate ORF peptide sequences in FASTA format.

Example¶

smorf_scanner \
  -g genome.fa \
  -a annotation.genePred \
  -o smorf.raw \
  -p smORF \
  -s ATG,CTG,GTG,TTG \
  -m 8 \
  -M 1000 \
  -x both \
  -u 6 \
  -d 6 \
  -O \
  -t 8

Notes¶

--scan-strand sense scans ORFs on the annotated transcript strand only.
--scan-strand antisense scans antisense transcript sequences.
--scan-strand both is useful when antisense ORFs are also of interest, but it may substantially increase the number of candidates.
--mark-overlap is recommended when downstream filtering should distinguish primary, nested, or overlapping candidates.
Scanner output is a candidate set. Use smorf_filter and smorf_evidence before prioritizing translated smORFs.