APPLES

APPLES a set of Perl scripts for analyzing promoter sequences in genomes.

Topic

Plant biology;Transcription factors and regulatory sites;Phylogenetics

Detail

  • Operation: Sequence feature detection

  • Software interface: Command-line user interface

  • Language: Perl

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: -

  • Credit: The authors thank Ben Hunt and Ezio Rosato for pre-publication access to the Euphausia superba Not1 transcript sequence. ND is a member of the Midlands Integrative Bioscience Training Programme funded by the Biotechnology and Biological Sciences Research Council (BBSRC) grant BB-J014532-1. PK was funded by BBSRC and ERASysBio + Grant BB-I004823-1. ET was funded by BBSRC grant BB-K001922-1.

  • Input: -

  • Output: -

  • Contact: Sascha Ott et22@le.ac.uk

  • Collection: -

  • Maturity: -

Publications

  • Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants
  • Baxter L, Jironkin A, Hickman R, Moore J, Barrington C, Krusche P, Dyer NP, Buchanan-Wollaston V, Tiskin A, Beynon J, Denby K, Ott S. Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. Plant Cell. 2012 Oct;24(10):3949-65. doi: 10.1105/tpc.112.103010. Epub 2012 Oct 30. PMID: 23110901; PMCID: PMC3517229.
  • https://doi.org/10.1105/tpc.112.103010
  • PMID: 23110901
  • PMC: PMC3517229
  • Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals.
  • Davies NJ, Krusche P, Tauber E, Ott S. Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals. BMC Evol Biol. 2015 Oct 19;15:227. doi: 10.1186/s12862-015-0499-6. PMID: 26482678; PMCID: PMC4613772.
  • https://doi.org/10.1186/s12862-015-0499-6
  • PMID: 26482678
  • PMC: PMC4613772

Download and documentation

    Currently not available or not maintained.

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