smORFer

smORFer is a computational tool to identify small open reading frames (smORFs) in prokaryotic genomes. These smORFs encode small proteins (≤50 amino acids) increasingly recognized as essential in various physiological processes. However, the systematic annotation of smORFs remains challenging due to the unique characteristics of prokaryotic genomes, such as polycistronic messages, overlapping ORFs, and non-canonical translation initiation.

smORFer addresses these challenges by employing an integrated approach that considers both the structural features of the genetic sequence and the evidence of in-frame translation from ribosome profiling (Ribo-Seq) data. The algorithm applies the Fourier transform to convert these parameters into a quantitative score, enabling the reliable selection of smORFs.

Topic

Cell biology;Gene transcripts;Protein expression;Model organisms;Physiology

Detail

  • Operation: Coding region prediction;Parsing;Repeat sequence organisation analysis;de Novo sequencing

  • Software interface: Command-line interface

  • Language: R,Shell,Perl

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: Deutsche Forschungsgemeinschaft, GRK PROCOMPAS.

  • Input: -

  • Output: -

  • Contact: Alexander Bartholomäus bartholomaeus.alexander@gmail.com ,Zoya Ignatova zoya.ignatova@chemie.uni-hamburg.de

  • Collection: -

  • Maturity: -

Publications

  • smORFer: a modular algorithm to detect small ORFs in prokaryotes.
  • Bartholomäus A, et al. smORFer: a modular algorithm to detect small ORFs in prokaryotes. smORFer: a modular algorithm to detect small ORFs in prokaryotes. 2021; 49:e89. doi: 10.1093/nar/gkab477
  • https://doi.org/10.1093/NAR/GKAB477
  • PMID: 34125903
  • PMC: PMC8421149

Download and documentation

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