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. Triticum dicoccoides (wild emmer wheat): WEWSeq v.1.0, WEW_v2.0
   • Article: Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. (WEWSeq v.1.0)
   • Article: Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps. (WEW_v2.0)
4. Aegilops tauschii: Aet v4.0
   • Article: Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.
5. Triticum turgidum L. ssp. durum: EBI-ENA PRJEBI-ENA (study PRJEB22687)EB22687
   • Article: Durum wheat genome highlights past domestication signatures and future improvement targets.
6. Triticum urartu: Tu2.0
   • Article: Genome sequence of the progenitor of wheat A subgenome Triticum urartu.
7. Brachypodium distachyon: v1.0
   • Article: Genome sequencing and analysis of the model grass Brachypodium distachyon.
8. Brachypodium distachyon v3.0: JGI v3.0 assembly of Brachypodium distachyon Bd21
   • Article: Genome sequencing and analysis of the model grass Brachypodium distachyon.
9. 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.
10. Zea mays: AGPv4
    • Article: Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.
11. Sweet potato (Ipomoea batatas): ipoBat4
12. Peanut
    • cultivated peanut, Arachis hypogaea cv. Tifrunner
    • diploid progenitor Arachis duranensis
    • diploid progenitor Arachis ipaensis
13. Sugar beet (Beta vulgaris): RefBeet-1.2.2
    • Article: The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).
14. Pummelo (Citrus grandis): Citrus grandis (L.) Osbeck.cv. 'Wanbaiyou' v1.0
    • Article: Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction.
15. Pyxicephalus adspersus: assembly_Pads_1.0
16. Pisum sativum : pea
17. Cotton
    • Gossypium arboreum (A2) SXY1 genome CRI-Updated v1_a1
    • Gossypium raimondii (D5) genome JGI v2_a2.1
    • Gossypium hirsutum (AD1) TM-1 genome ZJU-Improved v2.1_a1
18. Hexaploid OAT(OT3098 Hexaploid Oat): OAT_OT3098_V1,OAT_OT3098_V2
19. diploid OAT
    • Avena atlantica Genome sequence of the OAT A genome
    • Avena strigosa Genome sequence of the OAT A genome
    • Avena eriantha Genome sequence of the OAT C genome
    • Article: Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species.
    • Article: Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals (Avena spp.) diploid species.
20. diploid barley
    • Morex V2 barley_2.0
21. Weining_v01_rye
    • Weining_v01_rye diploid species.
    • Article: A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes
22. Secale_Lo7
    • Secale_Lo7 diploid species.
    • Article: Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential
23. Buckwheat
    • Fagopyrum tataricum (Tartary Buckwheat)
    • Article: The Tartary Buckwheat Genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance
24. Hordeum_marinum
    • Hordeum_marinum (Hordeum_marinum)
    • Article: The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies