realDB: A Genome Database for Red Algae

connecting real minds

Timeline for the sequenced genome & transcriptome

     The realDB V1.0, launched by Dr. Fei Chen and Dr. Liangsheng Zhang, maintains a database of genome and transcriptome data for the less represented red algae or the phylum Rhodophyta. Currently, realDB V1.0 provides the BLAST server, Jbrowse, and Download server and more, for easy accessing the ome data and omics tools representing all the 7 classes of red algae. Visitors are also welcome to submit their genome/transcriptome data regarding any red algae to realDB V1.0. Click anywhere to start your adventure!

  • Please cite us if you use realDB, your citation is very impportant to us to maintain and improve realDB.
  • URL: realDB.algaegenome.org
  • Publication: Fei Chen, Jiawei Zhang, Junhao Chen, Xiaojiang Li, Wei Dong, Jian Hu, Meigui Lin, Yanhui Liu, Zhengjia Wang, Liangsheng Zhang. realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta). Database. DOI: 10.1093/database/bay072
  • realDB V1.0


    • (03.06.2018) Transcription factor data for four flagship red algae were provided.
    • (12.05.2017) realDB V1.0 launched!

    realDB test version


    • (11.23.2017) realDB-beta version online! Very welcome to send us your comment: frank@fafu.edu.cn.
    • (06.29.2017) BLAST tools were developed.
    • (06.15.2017) geneSearch online! Start using it!
    • (06.08.2017) Jbrowse tools were implemented!
    • (05.28.2017) The red algae genome database realDB started!

    1. Dataset

    Species Data Type  Read Size Contig Number Assembled Size (Mb) Gene Models N50 Sequencing platform
    Ahnfeltiopsis flabelliformis Transcriptome 1.5Gb 22,183 32.6 18,933 2,748 Illumina HiSeq 2000
    Betaphycus philippinensis Transcriptome 1.8Gb 23,279 28.8 15,948 2,361 Illumina HiSeq 2000
    Ceramium kondoi Transcriptome 931.1Mb 23,126 21.4 18,402 1,385 Illumina HiSeq 2000
    Dumontia simplex Transcriptome 1.5Gb 18,910 22.5 15,572 2,048 Illumina HiSeq 2000
    Eucheuma denticulatum Transcriptome 1.7Gb 24,656 27.9 15,478 2,020 Illumina HiSeq 2000
    Gloiopeltis furcata Transcriptome 1.3Gb 24,860 25.9 18,359 1,594 Illumina HiSeq 2000
    Gracilaria blodgettii Transcriptome 735.2Mb 19,691 22.5 15,563 2,109 Illumina HiSeq 2000
    Gracilaria chouae Transcriptome 1.4Gb 14,597 25.8 16,438 2,904 Illumina HiSeq 2000
    Gracilaria vermiculophylla Transcriptome 2Gb 13,444 25.2 15,663 3,645 Illumina HiSeq 2000
    Grateloupia catenata Transcriptome 1.6Gb 27,157 29 18,190 2,015 Illumina HiSeq 2000
    Grateloupia filicina Transcriptome 1.5Gb 49,587 38.6 25,696 1,341 Illumina HiSeq 2000
    Grateloupia livida Transcriptome 1.3Gb 14,934 22.2 14,131 2440 Illumina HiSeq 2000
    Grateloupia turuturu Transcriptome 1.4Gb 15,739 25.5 15,639 2,591 Illumina HiSeq 2000
    Heterosiphonia pulchra Transcriptome 1.5Gb 33,225 28.6 19,183 1,594 Illumina HiSeq 2000
    Mazzaella japonica Transcriptome 1.4Gb 25,264 27 16,990 1,981 Illumina HiSeq 2000
    Neosiphonia japonica Transcriptome 1.3Gb 25,347 21.8 16,127 1,204 Illumina HiSeq 2000
    Porphyra purpurea  Transcriptome 869.9 Mb 20,323 24.8 655,453 1,121 454 GS FLX
    Compsopogon coeruleus Transcriptome 1015.8Mb 11,718 15.8 6,844 2,639 Illumina HiSeq 2000
    Erythrolobus madagascarensis Transcriptome 732.3Mb 14,099 14.5 9,152 1,433 Illumina HiSeq 2000
    Erythrolobus australicus Transcriptome 582.5Mb 14,227 15.4 11,857 1,533 Illumina HiSeq 2000
    Kappaphycus alvarezii Transcriptome 1.9Gb 34,095 40.8 20,253 1,550 Illumina HiSeq 2000
    Madagascaria erythrocladiodes Transcriptome 1.6Gb 51,999 48.9 39,931 1,041 Illumina HiSeq 2000
    Porphyridium aerugineum Transcriptome 1.2Gb 17,502 18 11,132 1,450 Illumina HiSeq 2000
    Rhodosorus marinus Transcriptome 1Gb 29,364 59.8 30,011 2,092 Illumina HiSeq 2000
    Rhodella maculata Transcriptome 1.5Gb 20,890 19.2 15,398 1,434 Illumina HiSeq 2000
    Timspurckia oligopyrenoides Transcriptome 1.5Gb 10,337 16.3 7,826 2,179 Illumina HiSeq 2000
    Symphyocladia latiuscula Transcriptome 939.5Mb 32,966 22 17,377 765 Illumina HiSeq 2000
    Galdieria phlegrea Genome 161Mb 11,559 13.7 10,303 1,467 454 GS FLX Titanium
    Porphyridium cruentum Genome 1.7Gb 7,321 29.3 17,005 9,536 Illumina Genome Analyzer Iix
    Gracilaria lemaneiformis Genome 2.8Gb 179,736 184 151,728 921 Illumina MiSeq
    Calliarthron tuberculosum Genome 1.6Gb 119,430 99.7 28,266 718 454 GS FLX Titanium
    Chondrus crispus Genome 1.7Gb 925 104.8 9,606 240 Sanger technology
    Cyanidioschyzon merolae Genome 1.8Gb 20 15.9 5,331 859,119 whole genome random sequencing
    Galdieria sulphuraria Genome 60Mb 117 12 7,174 134,001 ONT MinION
    Porphyra umbilicalis Genome 558.41Gb 2,126 85.1 14,399 202,021 PacBio RS
    Porphyridium purpureum Genome 7Gb 3,014 19.45 7,730 20,534 Illumina GAIIx
    Pyropia yezoensis Genome 1.9Gb 44,634 42.7 10,327 1,669 Illumina Genome Analyzer Iix

    2. Powerful bioinformatics tools for online analysis

    • 1. Powerful BLAST suit: BLASTp, BLASTn, tBLASTn, BLASTX. For advanced BLAST, 23 parameters are optional.
    • 2. Search systems for genes, proteins, miRNAs, et al.
    • 3. Jbrowse for four flagship genomes.
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