PETadex index repo

October 10, 2025 · View on GitHub

PETAdexR

PETadexR [link] provides R based data exploration and analysis tools for plastic‑degrading enzyme sequences. Leveraging petabase‑scale computational biology and high‑throughput functional genomics, PETadexR helps bioinformaticians and biologists identify, visualize, and prioritize novel PETase homologs for experimental validation.

PETadex.io [Under construction]

PETadex.io [link] is the repository for the `PETadex website.

PETadex Data-lake (s3://petadex/)

PETadex-logan sequences are hosted on S3, accessible via aws cli or wget of URL paths below. [ Bug Fix: 2025-10-10. Allowed unsigned cli access, added URL access]

s3://petadex/logan
├── # PETadex-Logan ========================================================
├── petadex.logan.enz.v1.fa.zst          # PETadex-Logan Enzymes (18.6 GiB)
├── petadex.logan.seq.v1.fa.zst          # Logan Sequence Matches (61.4 GiB)
├── petadex.logan.all_orfs.v1.fa.zst     # Logan search hits (120.3 GiB)
├── # PETadex-nr ===========================================================
├── petadex.nr.enz.fa.zst                # PETadex-nr Enzymes (144 MB)
├── petadex.nr.seq.fa.zst                # NCBI nr hits (207 MB)
├── petadex.nr.seqcluster.tsv.zst        # PETAdex-nr clustering (38 MB)
├── # Halo Assay ===========================================================
├── haloAssay/
    ├── logan.haloAssay.v250729.xlsx    # Halo Assay spreadsheet
    ├── logan.haloAssay.norm.tsv.zst    # Normalized halo assay
    ├── logan.haloAssay.raw.tsv.zst     # Raw halo assay quantification
    └── logan.haloAssay.v241123.msta.fa # Structural alignment of synth. enzy

PETadex Logan Enzymes (clustered 90%aaid) : petadex.logan.enz.v1.fa.zst (18.6 GiB)

Filtered Petadex-Logan sequences (aa) clustered against NCBI nr centroids, and then themselves

  • aws s3 cp s3://petadex/logan/petadex.logan.enz.v1.fa.zst ./ (preferred)
  • wget https://petadex.s3.us-east-1.amazonaws.com/logan/petadex.logan.enz.v1.fa.zst
  • Download Link

PETadex Logan Sequences: petadex.logan.seq.v1.fa.zst (61.4 GiB)

Logan sequences passing HMM-filtering and coverage criteria for inclusion.

  • aws s3 cp s3://petadex/logan/petadex.logan.seq.v1.fa.zst ./ (preferred)
  • wget https://petadex.s3.us-east-1.amazonaws.com/logan/petadex.logan.seq.v1.fa.zst
  • Download Link

Raw Logan Sequences: petadex.logan.all_orfs.v1.fa.zst (120.3 GiB)

Raw logan sequences (amino-acid) aligning to petadex-nr. For accessing the nucleotide contigs see: Logan Contigs

  • aws s3 cp s3://petadex/logan/petadex.logan.all_orfs.v1.fa.zst ./ (preferred)
  • wget https://petadex.s3.us-east-1.amazonaws.com/logan/petadex.logan.all_orfs.v1.fa.zst
  • Download Link

PETadex NR Enzymes (clustered 90%aaid) : petadex.nr.enz.fa.zst (144 MB)

Filtered and clustered Petadex-nr sequences (aa) from NCBI nr. Search query for Logan.

  • aws s3 cp s3://petadex/logan/petadex.nr.enz.fa.zst ./ (preferred)
  • wget https://petadex.s3.us-east-1.amazonaws.com/logan/petadex.nr.enz.fa.zst
  • Download Link

PETadex Halo Assay Data : haloAssay/logan.haloAssay.v250729.xlsx (3 MB)

Halo Assay data. Raw, Noramlized/Aggregated values, and synthesized sequences.

  • aws s3 cp s3://petadex/logan/haloAssay/logan.haloAssay.v250729.xlsx ./ (preferred)
  • wget https://petadex.s3.us-east-1.amazonaws.com/logan/haloAssay/logan.haloAssay.v250729.xlsx
  • Download Link