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  • GENCODE - Ribo-seq ORFs
    In recent years, Ribosome Profiling (Ribo-seq) has been used to detect thousands of non-canonical – i e unannotated – translated open reading frames (ORFs) in the human genome GENCODE are working on a long-term community-driven project to incorporate these features into reference gene annotation
  • GENCODE - Home page
    The GENCODE Primary transcript set captures a minimal set of transcripts at protein coding genes GENCODE are supporting the annotation of non-canonical human ORFs predicted by Ribo-seq data, now including the integration of peptidomics and immunopeptidomics data
  • Expanding the human proteome with microproteins and peptideins
    We began with every ATG-initiated ORF of any length in any protein-coding or lncRNA transcript in GENCODE v42 that did not overlap a protein-coding CDS of any transcript in the same frame
  • GitHub - jorruior gencode-riboseqORFs: Python script to get an unified . . .
    While this script is designed to unify independent sets of ORFs and map them to a specific Ensembl version, it is not a tool to analyze ribosome-profiling data However, GENCODE plans to develop a Phase II to re-analyze ribosome-profiling datasets and call ORFs
  • Standardized annotation of translated open reading frames
    Here, we outline a community-led effort involving Ensembl GENCODE, the HUGO Gene Nomenclature Committee (HGNC), UniProtKB, HUPO HPP and PeptideAtlas to produce a standardized catalog of 7,264
  • Evolutionary remodeling of non-canonical ORF translation in mammals
    Non-canonical open reading frames (ncORFs) are pervasive within transcripts annotated as “non-coding” or “untranslated regions” of mRNAs, yet their landscape under normal physiological conditions remains to be fully resolved, particularly outside humans
  • gencode-riboseqORFs README. md at main · jorruior gencode . . . - GitHub
    These files can be downloaded from Ensembl or GENCODE; we also included a bash script to automatically download and convert all files for a specific Ensembl release:
  • expanded reference catalog of translated open reading frames for . . .
    Here, we present an expanded and refined catalog of the human reference annotation of ncORFs By incorporating more datasets and by lifting constraints on ORF length and start codon, we define a comprehensive set of 28 359 ncORFs that is nearly four times the size of the previous catalog
  • nuORFdb - proteomics. broadinstitute. org
    The Riboseq data from all samples was combined via our hierarchical ORF prediction pipeline, where ORFs were predicted at multiple nodes, consisting of each sample (leaf), tissue (clade) and across all samples combined (root)
  • ORF Finder - bamboo. genobank. org
    Open Reading Frame (ORF) Finder Example Data Enter Query Sequence Enter nucleotide sequence in FASTA format:





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