Bioinformatics Tools

Analyse your own sequences and taxa against PlasticDB.

Overview

PlasticDB provides several analysis pipelines. Most align your input against the PlasticDB enzyme database with DIAMOND (a fast BLAST alternative) and, where relevant, predict signal peptides with SignalP 5.0. One tool instead matches taxonomy names, and two build phylogenetic trees. Jobs run asynchronously — you can close the page and check back later under My Jobs.

Running a job requires a (free) account, except Build Phylogenetic Tree, which is open to everyone. All tools are reachable from the Tools menu.

Sequence-based tools (DIAMOND)

Annotate Gene

/tools/annotate-gene — paste a single protein or nucleotide sequence to find its closest PlasticDB matches. Supports BLASTP (protein) and BLASTX (nucleotide, translated in all six frames), with SignalP 5.0 signal-peptide prediction.

Annotate Genome

/tools/annotate-genome — upload a multi-FASTA file of predicted proteins from a genome. Each sequence is aligned independently against PlasticDB to surface every candidate plastic-degrading gene. Best for whole-genome annotation.

Compare Genomes

/tools/compare-genomes — upload several FASTA files (one per genome or metagenome) and compare their enzyme-hit profiles as a matrix, broken down by plastic type. Useful for contrasting the plastic-degrading potential of different strains or communities.

Pathway Analysis

/tools/pathway-analysis — upload a multi-FASTA file to map your sequences onto the Pseudideonella sakaiensis PET-degradation pathway; hits light up the steps they cover on a pathway diagram. This tool is currently PET-specific.

Taxonomy-based tool

Annotate Taxa Table

/tools/annotate-list — upload a taxonomy table (for example DADA2/QIIME2 output) with genus and species columns. Rather than aligning sequences, this tool resolves the taxon names against NCBI Taxonomy and reports which of your taxa are known plastic-degrading organisms in PlasticDB. Use it to scan microbiome or environmental survey data for plastic-degrading taxa.

Phylogenetic trees

/tools/build-tree (public) builds a phylogenetic tree from a filtered set of PlasticDB microorganisms, and the Interactive Tree lets you explore the taxonomy of the whole database visually.

Common parameters

  • E-value — significance threshold; lower is more stringent. Default 1e-5. For exploratory searches, loosen towards 1e-3.
  • Percent identity — minimum amino-acid identity. Default 30%. Raise to 60–70% for near-exact matches.
  • Organism type — SignalP prediction mode: Gram-positive, Gram-negative, Archaea, Eukaryotic, or no prediction.
  • BLAST type — BLASTP for protein input, BLASTX for nucleotide input (translated in six frames).
  • Compressed input — every upload control accepts gzip. Upload genome.fasta.gz as-is; it is stored compressed and read directly by the search engines, and results are labelled genome.

Running jobs well

  1. Choose the right tool — Annotate Gene for a single sequence, Annotate Genome for whole genomes, Annotate Taxa Table for taxonomic surveys.
  2. Check your input format — multi-FASTA files need valid > headers; taxa tables need genus and species columns.
  3. Be patient — large files can take several minutes. Jobs run in the background; track them from My Jobs.
  4. Read results critically — a hit with low identity (30–40%) may not indicate genuine plastic-degrading activity. Cross-reference with the literature and the evidence on each PlasticDB match.

These tools are also available programmatically via the Jobs API — see the REST API page.