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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 38334 1521 algae.tar.gz 07-11-2022
    alveolates 21 207674 51205 1132 alveolates.tar.gz 07-11-2022
    amoebozoa 7 81844 22114 1165 amoebozoa.tar.gz 07-11-2022
    amphibians 3 75261 17186 13925 amphibians.tar.gz 07-11-2022
    animals 370 7150735 270089 1512 animals.tar.gz 07-11-2022
    apicomplexans 18 93576 14632 1091 apicomplexans.tar.gz 07-11-2022
    arthropods 119 1727651 113673 5106 arthropods.tar.gz 07-11-2022
    ascomycetes 100 904642 98151 2799 ascomycetes.tar.gz 07-11-2022
    basidiomycetes 33 363997 56935 2453 basidiomycetes.tar.gz 07-11-2022
    birds 31 482205 22397 11761 birds.tar.gz 07-11-2022
    cnidarians 9 203000 24003 5547 cnidarians.tar.gz 07-11-2022
    crustaceans 7 154960 37407 5216 crustaceans.tar.gz 07-11-2022
    dothideomycetes 10 123200 28898 5567 dothideomycetes.tar.gz 07-11-2022
    eudicots 93 3180221 102679 8230 eudicots.tar.gz 07-11-2022
    euglenozoa 9 86483 12363 4638 euglenozoa.tar.gz 07-11-2022
    eurotiomycetes 20 196228 25710 4723 eurotiomycetes.tar.gz 07-11-2022
    fishes 64 1736572 43690 13248 fishes.tar.gz 07-11-2022
    flatworms 4 58181 17784 4237 flatworms.tar.gz 07-11-2022
    fungi 138 1278312 148080 2138 fungi.tar.gz 07-11-2022
    insects 101 1376824 70170 5971 insects.tar.gz 07-11-2022
    leotiomycetes 5 67865 21669 5707 leotiomycetes.tar.gz 07-11-2022
    mammals 94 1910363 47144 14776 mammals.tar.gz 07-11-2022
    mollusks 9 206905 35775 6726 mollusks.tar.gz 07-11-2022
    monocots 17 560027 43452 9611 monocots.tar.gz 07-11-2022
    nematodes 6 134093 35865 3280 nematodes.tar.gz 07-11-2022
    plants 127 3968027 162990 3485 plants.tar.gz 07-11-2022
    protists 52 660237 134452 602 protists.tar.gz 07-11-2022
    reptiles 20 384584 21725 12715 reptiles.tar.gz 07-11-2022
    saccharomycetes 36 195913 14873 3079 saccharomycetes.tar.gz 07-11-2022
    stramenopiles 8 119746 31582 567 stramenopiles.tar.gz 07-11-2022
    vertebrates 212 4588985 83704 8222 vertebrates.tar.gz 07-11-2022

  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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