This repository contains the source code for the CyVerse/iPlant version of the APPLES (Analysis of Plant Promoter-Linked Elements) application package. The APPLES software package is a set of tools to analyse promoter sequences on a genome-wide scale.
Two functionalities are provided in this version:
Finding Orthologs as Reciprocal Best Hits (rbh-apples)
Finding Non-Coding Conserved Regions (conservation-apples)
Details of this version of APPLES will be added here later. In the meantime, you can find more about the original APPLES following this link, and please check out our papers:
Nathaniel J. Davies, Peter Krusche, Eran Tauber and Sascha Ott, Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals, BMC Evolutionary Biology, 2015, doi: 10.1186/s12862-015-0499-6
Laura Baxter, Aleksey Jironkin, Richard Hickman, Jay Moore, Christopher Barrington, Peter Krusche, Nigel P. Dyer, Vicky Buchanan-Wollaston, Alexander Tiskin, Jim Beynon, Katherine Denby, and Sascha Ott, Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants, Plant Cell, 2012, doi:10.1105/tpc.112.103010