About B2DSC

This server is in Dr. Zujun Yang Lab at School of Life Science and Technology, University of Electronic Science and Technology of China.

Originally, B2DSC was established to provide a view of the distribution of the homologous sequences of several oligonucleotide probes on chromosomes, mainly for wheat research. Based on the newly released IWGSC RefSeq v1.0 of bread wheat variety Chinese Spring, which is an assembly of high-quality, we can get the general distribution of repeated sequences in the genome, then do a plot to view it.

Dependency

B2DSC mainly depends on:

1. blastn in NCBI-BLAST+ suite (v2.2.30+).
2. Perl real-time web framework Mojolicious (v6.15).
3. Bio::SeqIO of BioPerl and other Perl modules (e.g. JSON and several core modules).
4. Faidx of this server. Which provides a web interface for the Samtools (v0.1.19) command faidx.
5. JavaScript libraries
   • jQuery: A fast, small, and feature-rich JavaScript library (v3.1.1).
   • D3.js: a JavaScript library for manipulating documents based on data. (v4.8.0).
   • Spectrum.js: The No Hassle JavaScript Colorpicker (v1.8.0).
   • FileSaver.js: An HTML5 saveAs() FileSaver implementation.

Source of BLAST databases

1. Wheat (Triticum aestivum): IWGSC RefSeq v1.0
2. Barley (Hordeum vulgare): IBSC (2016-07-14): Pseudomolecules of the map-based reference genome assembly of barley cv. Morex. DOI:10.5447/IPK/2016/34
   • Article: A chromosome conformation capture ordered sequence of the barley genome
3. Brachypodium distachyon: v1.0
   • Article: Genome sequencing and analysis of the model grass Brachypodium distachyon.
4. Brachypodium distachyon v3.0: JGI v3.0 assembly of Brachypodium distachyon Bd21
   • Article: Genome sequencing and analysis of the model grass Brachypodium distachyon.
5. Oryza sativa Indica: Oryza sativa Indica Group cultivar:Shuhui498 (long-grained rice)
   • Article: Sequencing and de novo assembly of a near complete indica rice genome.
6. Zea mays: AGPv4
   • Article: Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.
7. Triticum dicoccoides (wild emmer wheat): NCBI-Assembly WEWSeq v.1.0
   • Article: Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.
8. Aegilops tauschii: Aet v4.0
   • Article: Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.
9. Triticum urartu: Tu2.0
   • Article: Genome sequence of the progenitor of wheat A subgenome Triticum urartu.
10. Sweet potato (Ipomoea batatas): ipoBat4
11. Peanut
    • cultivated peanut, Arachis hypogaea cv. Tifrunner
    • diploid progenitor Arachis duranensis
    • diploid progenitor Arachis ipaensis