Investigating open reading frames in known and novel transcripts using ORFanage

No country for old methods: New tools for studying microproteins

“…A pseudo-alignment algorithm, named ORFanage, was recently established for the detection of novel ORFs in the assembled results from RNA-seq. 58 ORFanage can identify ORFs from RNA-seq data based on the similarity to the reference annotation and similarity within genes in the transcripts. 58 The method relies on the assumption that protein-coding genes produced by different transcripts from the same locus should share similarities, which are then exploited to detect new microproteins.…”

“… 58 The method relies on the assumption that protein-coding genes produced by different transcripts from the same locus should share similarities, which are then exploited to detect new microproteins. 58 …”

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

“…Only transcripts that were assembled directly from the individual samples and from “TieBrush”-ed files were retained, and further filtered with an intron classifier designed to recognize introns that resemble most the introns in the reference annotation. ORFanage [ 18 ] and ColabFold were used to assign and score ORFs to protein-coding transcripts, and pLDDT scores produced by ColabFold were used to filter out low-scoring protein-coding transcripts …”

“…These steps reduced the dataset to 160,482 transcripts, of which 97,661 were protein-coding. All of the protein-coding transcripts were assigned coding sequence (CDS) features either by copying them from matching RefSeq transcripts, where available, or by the ORFanage [ 18 ] program as described in Additional file 2 : Supplementary Methods. For the sake of discussion, we call these the “Beta” proteins here.…”