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sORFs.org : a repository of small ORFs identified by ribosome profiling

Volodimir Olexiouk (UGent) , Jeroen Crappé (UGent) , Steven Verbruggen (UGent) , Kenneth Verheggen (UGent) , Lennart Martens (UGent) and Gerben Menschaert (UGent)
(2015) NUCLEIC ACIDS RESEARCH. 44(D1). p.D324-D329
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Abstract
With the advent of ribosome profiling, a next generation sequencing technique providing a ‘snap-shot’ of translated mRNA in a cell, many short open reading frames (sORFs) with were identified. Follow-up studies revealed the existence of functional peptides, so-called micropeptides, translated from these ‘sORFs’, indicating a new class of bio-active peptides. Over the last few years, several micropeptides exhibiting important cellular functions were discovered. However, ribosome occupancy does not necessarily imply an actual function of the translated peptide, leading to the development of various tools assessing the coding potential of sORFs. Here, we introduce sORFs.org (http://www.sorfs.org), a novel database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14_mESC (mouse) and S2 (fruit fly). sORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects.
Keywords
PRIDE, PEPTIDES, TRANSLATION, IN-VIVO, NUCLEOTIDE RESOLUTION, OPEN READING FRAMES, micropeptide, smorf, small open reading frame, sorf, ribosome profiling, UCSC GENOME BROWSER, RIBO-SEQ, CONSERVATION, UNIPROT, DATABASE

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Chicago
Olexiouk, Volodimir, Jeroen Crappé, Steven Verbruggen, Kenneth Verheggen, Lennart Martens, and Gerben Menschaert. 2015. “sORFs.org : a Repository of Small ORFs Identified by Ribosome Profiling.” Nucleic Acids Research 44 (D1): D324–D329.
APA
Olexiouk, V., Crappé, J., Verbruggen, S., Verheggen, K., Martens, L., & Menschaert, G. (2015). sORFs.org : a repository of small ORFs identified by ribosome profiling. NUCLEIC ACIDS RESEARCH, 44(D1), D324–D329.
Vancouver
1.
Olexiouk V, Crappé J, Verbruggen S, Verheggen K, Martens L, Menschaert G. sORFs.org : a repository of small ORFs identified by ribosome profiling. NUCLEIC ACIDS RESEARCH. 2015;44(D1):D324–D329.
MLA
Olexiouk, Volodimir, Jeroen Crappé, Steven Verbruggen, et al. “sORFs.org : a Repository of Small ORFs Identified by Ribosome Profiling.” NUCLEIC ACIDS RESEARCH 44.D1 (2015): D324–D329. Print.
@article{6974248,
  abstract     = {With the advent of ribosome profiling, a next generation sequencing technique providing a {\textquoteleft}snap-shot{\textquoteright} of translated mRNA in a cell, many short open reading frames (sORFs) with were identified. Follow-up studies revealed the existence of functional peptides, so-called micropeptides, translated from these {\textquoteleft}sORFs{\textquoteright}, indicating a new class of bio-active peptides. Over the last few years, several micropeptides exhibiting important cellular functions were discovered. However, ribosome occupancy does not necessarily imply an actual function of the translated peptide, leading to the development of various tools assessing the coding potential of sORFs. Here, we introduce sORFs.org (http://www.sorfs.org), a novel database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14\_mESC (mouse) and S2 (fruit fly). sORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects.},
  author       = {Olexiouk, Volodimir and Crapp{\'e}, Jeroen and Verbruggen, Steven and Verheggen, Kenneth and Martens, Lennart and Menschaert, Gerben},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  language     = {eng},
  number       = {D1},
  pages        = {D324--D329},
  title        = {sORFs.org : a repository of small ORFs identified by ribosome profiling},
  url          = {http://dx.doi.org/10.1093/nar/gkv1175},
  volume       = {44},
  year         = {2015},
}

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