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Frequently Asked Questions

  1. What are the organisms/organism groups supported by EcoOmicsAnalyst?
  2. How is your raw RNA-seq data processed?
  3. What version of Seq2Fun does EcoOmicsAnalyst use?
  1. What are the organisms/organism groups supported by EcoOmicsAnalyst?

    We currently provide databases for ~30 organism groups. Please check here for more details on how Seq2Fun works. All databases can be downloaded here.
    Note: the ortholog includes all genes (including genes are not orthology with any other genes) from that groups of organisms.
    Groups of organisms can be download from (here).

    The definition of a core ortholog is that its frequency in the group >= 0.90. This is in consistent with BUSCO
    Note: * frequency >= 0.85; ** frequency >= 0.80;

    Group Species Proteins Ortholog Core ortholog Filename Date
    Algae 14 155495 34628 1831 algae.tar.gz 03-02-2022
    alveolates 21 207674 48656 1099 alveolates.tar.gz 03-02-2022
    amoebozoa 7 81844 20217 1200 amoebozoa.tar.gz 03-02-2022
    amphibians 3 75261 9838 7776 amphibians.tar.gz 03-02-2022
    animals 370 7150735 236447 3388 animals.tar.gz 03-02-2022
    apicomplexans 18 93576 13823 1042 apicomplexans.tar.gz 03-02-2022
    arthropods 119 1727651 101867 4053 arthropods.tar.gz 03-02-2022
    ascomycetes 100 904642 93433 2590 ascomycetes.tar.gz 03-02-2022
    basidiomycetes 33 363997 52723 2263 basidiomycetes.tar.gz 03-02-2022
    birds 31 482205 13868 6433 birds.tar.gz 03-02-2022
    cnidarians 9 203000 18682 4840 cnidarians.tar.gz 03-02-2022
    crustaceans 7 154960 32225 4408* crustaceans.tar.gz 03-02-2022
    dothideomycetes 10 123200 26288 4644 dothideomycetes.tar.gz 03-02-2022
    eudicots 93 3180221 72086 6935 eudicots.tar.gz 03-02-2022
    euglenozoa 9 86483 11790 4341 euglenozoa.tar.gz 03-02-2022
    eurotiomycetes 20 196228 23006 4081 eurotiomycetes.tar.gz 03-02-2022
    fishes 64 1736572 27327 7140 fishes.tar.gz 03-02-2022
    flatworms 4 58181 15156 3720 flatworms.tar.gz 03-02-2022
    fungi 138 1278312 141223 2063 fungi.tar.gz 03-02-2022
    insects 101 1376824 60375 4508 insects.tar.gz 03-02-2022
    leotiomycetes 5 67865 19335 4833 leotiomycetes.tar.gz 03-02-2022
    mammals 94 1910363 32471 7781* mammals.tar.gz 03-02-2022
    mollusks 9 206905 29992 5485** mollusks.tar.gz 03-02-2022
    monocots 17 560027 32745 6060 monocots.tar.gz 03-02-2022
    nematodes 6 134093 32549 3018 nematodes.tar.gz 03-02-2022
    plants 127 3968027 128122 3872 plants.tar.gz 03-02-2022
    protists 52 660237 126969 736 protists.tar.gz 03-02-2022
    reptiles 20 384584 11946 6786 reptiles.tar.gz 03-02-2022
    saccharomycetes 36 195913 13337 2741 saccharomycetes.tar.gz 03-02-2022
    stramenopiles 8 119746 28902 680 stramenopiles.tar.gz 03-02-2022
    vertebrates 212 4588985 59392 6045 vertebrates.tar.gz 03-02-2022

  2. How is the raw RNA-seq data processed?

    EcoOmicsAnalyst has 3 main steps to process raw RNA-sq data for species without a reference genome. The following steps are all done using the Seq2Fun software.

    1. Raw reads quality control, including adopter detection removal, low quality reads and bases removal, error correction. Raw Reads quality control will remove low quality and too short reads; trim low quality bases; remove sequencing adapters, ploy(A) tails, low complex reads; perform error correction for overlapped region of paired-end reads and join the overlapped paired-end reads.
    2. Clean reads alignment via translated search in a protein ortholog database. Each clean read will be translated into all possible amino acid sequences using the six reading-frames and the top longest ones will be used to identify its homology sequence in the protein database.
    3. Summarize results into gene abundance tables, figures. The gene/ortholog abundance table is generated by summarizing all reads that are mapped to the same ortholog group.

    Click here, read our paper (Peng Liu, et al. (2021), or check the Workflow tab for more details.

  3. What version of Seq2Fun does EcoOmicsAnalyst use?

    EcoOmicsAnalyst uses version 2.0.2 of Seq2Fun. All previous versions of Seq2Fun are still available for commandline use. Go to www.seq2fun.ca to download and install previous versions.

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