Bartholomäus et al. 2021 (PRJNA632889)

General Details

Title smORFer: a modular algorithm to detect small ORFs in prokaryotes
Organism
Number of Samples 2
Release Date 2020/05/14 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP261663
ENA SRP261663
GEO
BioProject PRJNA632889

Publication

Title
Authors Bartholomäus A,Kolte B,Mustafayeva A,Goebel I,Fuchs S,Benndorf D,Engelmann S,Ignatova Z
Journal Nucleic acids research
Publication Date 2021 Sep 7
Abstract Emerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of their cognate small open-reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Multiple identifiers of ORFs that use the 3-nt periodicity in Ribo-Seq data sets have been successful in eukaryotic smORF annotation. They have difficulties evaluating prokaryotic genomes due to the unique architecture (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.). Here, we present a new algorithm, smORFer, which performs with high accuracy in prokaryotic organisms in detecting putative smORFs. The unique feature of smORFer is that it uses an integrated approach and considers structural features of the genetic sequence along with in-frame translation and uses Fourier transform to convert these parameters into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way, and dependent on the data available for a particular organism, different modules can be selected for smORF search. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
PMC PMC8421149
PMID 34125903
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR11791220 PRJNA632889 Staphylococcus aureus Ribo-Seq
SRR11791221 PRJNA632889 Staphylococcus aureus Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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