cyversewarwick/apples_rbh repository overview

⁠APPLES (Analysis of Plant Promoter-Linked Elements)

⁠Introduction

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