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Figure 1 | BMC Bioinformatics

Figure 1

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

Figure 1

Screenshots of the search, alignment and help pages of uPEPperoni. (A) The conserved uPEP search page showing the user-selectable settings for the RefSeq database, Ka/Ks ratio, reference heatmaps, alignment parameters and heatmap generation. (B) The heatmap alignment page showing the user-selectable settings for visual representation of the main coding sequence (CDS) and uORFs and the search parameters for uORF-length, the extent of uORF overlap into the CDS and the region of the transcript to be searched. (C) The help page. uPEPperoni is hosted on an Apache server on a Linux platform and is publically accessible free of charge at http://upep-scmb.biosci.uq.edu.au. Full documentation of uPEPperoni is also accessible via links on the website. The uORF reference database is automatically rebuilt on the server shortly after each major RefSeq release. We archive previous uORF reference databases. The RefSeq release version number from which the reference database is derived is shown on the web page.

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