uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation

Skarshewski, Adam, Stanton-Cook, Mitchell, Huber, Thomas, Al Mansoori, Sumaya, Smith, Ross, Beatson, Scott A. and Rothnagel, Joseph A. (2014) uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation. BMC Bioinformatics, 15 36: 1-6. doi:10.1186/1471-2105-15-36

Author Skarshewski, Adam
Stanton-Cook, Mitchell
Huber, Thomas
Al Mansoori, Sumaya
Smith, Ross
Beatson, Scott A.
Rothnagel, Joseph A.
Title uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation
Journal name BMC Bioinformatics   Check publisher's open access policy
ISSN 1471-2105
Publication date 2014-02-01
Sub-type Article (original research)
DOI 10.1186/1471-2105-15-36
Open Access Status DOI
Volume 15
Issue 36
Start page 1
End page 6
Total pages 6
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
Background Several small open reading frames located within the 5′ untranslated regions of mRNAs have recently been shown to be translated. In humans, about 50% of mRNAs contain at least one upstream open reading frame representing a large resource of coding potential. We propose that some upstream open reading frames encode peptides that are functional and contribute to proteome complexity in humans and other organisms. We use the term uPEPs to describe peptides encoded by upstream open reading frames.

Results We have developed an online tool, termed uPEPperoni, to facilitate the identification of putative bioactive peptides. uPEPperoni detects conserved upstream open reading frames in eukaryotic transcripts by comparing query nucleotide sequences against mRNA sequences within the NCBI RefSeq database. The algorithm first locates the main coding sequence and then searches for open reading frames 5′ to the main start codon which are subsequently analysed for conservation. uPEPperoni also determines the substitution frequency for both the upstream open reading frames and the main coding sequence. In addition, the uPEPperoni tool produces sequence identity heatmaps which allow rapid visual inspection of conserved regions in paired mRNAs.

Conclusions uPEPperoni features user-nominated settings including, nucleotide match/mismatch, gap penalties, Ka/Ks ratios and output mode. The heatmap output shows levels of identity between any two sequences and provides easy recognition of conserved regions. Furthermore, this web tool allows comparison of evolutionary pressures acting on the upstream open reading frame against other regions of the mRNA. Additionally, the heatmap web applet can also be used to visualise the degree of conservation in any pair of sequences. uPEPperoni is freely available on an interactive web server at http://upep-scmb.biosci.uq.edu.au
Keyword 5′UTR
Sequence conservation
Short peptides
Homology heatmaps
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Chemistry and Molecular Biosciences
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Citation counts: TR Web of Science Citation Count  Cited 5 times in Thomson Reuters Web of Science Article | Citations
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Created: Fri, 14 Feb 2014, 20:50:44 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences