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cdBEST: chromatin domain Boundary Element Search Tool
What is cdBEST?
cdBEST is a tool/software developed in Perl to search the chromatin domain boundary element sequences in 12 Drosophila species. cdBEST uses recognition sequences of boundary interacting proteins and looks for ‘motif clusters’ under a set of constrains to predict boundary element sequences. Apart from Drosophila, cdBEST can be used in several other insect genomes, where the boundary interacting proteins are conserved.

  • Arumugam Srinivasan and Rakesh K Mishra.
    Chromatin domain boundary element search tool for Drosophila.
    Nucleic Acids Res. 40 (10), 4385-4395, 2012 [PubMed ] [FREE Full Text]
  • Sajad H. Ahanger, Arumugam Srinivasan, Dasari Vasanthi, Yogesh S. Shouche and Rakesh K Mishra.
    Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae.
    Nucleic Acids Res. 41 (2), 804-816, 2013 [PubMed ] [FREE Full Text]
cdBEST varients and their sytem requirements:
The cdBEST is available as two variants, cdBEST_basic and cdBEST_advanced.
1. cdBEST_basic
The basic version is a command line Perl script requires Perl alone, can be used in Linux and Mac computers directly without any additional requirements. Microsoft Windows computers require Perl to be installed. cdBEST_basic uses FASTA formatted sequence file and produces four different text output files.
2. cdBEST_advanced
This version offers a simple Graphical User Interface (click here for screenshots), which allows the users to change various set parameters to searching boundaries including window size, etc. In addition to text output files, this version generates image output file showing boundaries and gene annotations together(click here for screenshots). Using this version, one can generate text files that can be uploaded to genome browsers such as FlyBase GBrowse and UCSC genome browser. Apart from boundary search this version can be used for searching the binding motifs of individual boundary proteins such as GAF, CTCF, etc. The cdBEST_advanced_v1.0 requires PerlTk module andBioPerl for all Operating System (OS) platforms.
Download cdBEST:
You should download the source file that suits you. Unzip the downloaded file in your system and follw the readme file, that is provided along with each souce file to install.
  Windows Mac OS Linux
cdBEST_basic basic_v1.0.zip basic_v1.0.zip basic_v1.0.zip
cdBEST_advanced_with_bioperl_library advanced_v1.0.zip advanced_v1.0.zip advanced_v1.0.zip

You may download Perl from ActiveState site.

If you are new to Perl and want to use cdBEST_advanced, we suggest you to try in Windows Operating System with ActiveState Perl installation. As it is very convenient and doesn't require any additional expertise to install Perl and other required modules.

If you have any further queries regarding installation, please contact asrini@ccmb.res.in

12 Drosophila species Boundary Element Search Data

We have used 12 Drosophila species genomes for boundary search.The results can be downloaded by following the links provided bleow.

Species All Data FlyBase GBrowse
custom tracks
BED Files
(to use as custom tracks)
Drosophila melanogaster (R5.37) melanogaster_all.zip gbrowse.zip mel.bed
Drosophila simulans (R1.3) simulans_all.zip gbrowse.zip sim.bed*
Drosophila sechellia (R1.3) sechellia_all.zip gbrowse.zip sec.bed*
Drosophila yakuba (R1.3) yakuba_all.zip gbrowse.zip yak.bed*
Drosophila erecta (R1.3) erecta_all.zip gbrowse.zip ere.bed*
Drosophila ananassae (R1.3) ananassae_all.zip gbrowse.zip ana.bed*
Drosophila pseudoobscura (R2.20) pseudoobscura_all.zip gbrowse.zip pse.bed*
Drosophila persimilis (R1.3) persimilis_all.zip gbrowse.zip per.bed*
Drosophila willistoni (R1.3) willistoni_all.zip gbrowse.zip wil.bed*
Drosophila mojavensis (R1.3) mojavensis_all.zip gbrowse.zip moj.bed*
Drosophila virilis (R1.2) virilis_all.zip gbrowse.zip vir.bed*
Drosophila grimshawi (R1.3) grimshawi_all.zip gbrowse.zip gri.bed*

*Since, the UCSC genome browser uses the previous version of the genome releases for these species; presently these bed files cannot be used as custom tracks there.

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