Gene calling

Gene calling predicts protein-coding genes (open reading frames) in bacterial genome sequences. Sparrowhawk offers this through Orphos, a Rust port of Prodigal (paper), a widely-used prokaryotic gene predictor.

General considerations

• Accepts FASTA files (plain or gzipped). Multiple files can be processed in parallel across workers.
• Two operating modes:
  • Single-genome mode (default, metag=false): all contigs in a file are first concatenated (separated by stop-codon bridges) to train the gene model on the whole genome, then each contig is analysed independently with that trained model. Best for complete or near-complete assemblies.
  • Metagenomic mode (metag=true), also called anonymous: each contig is analysed independently with a pre-trained general model. Recommended for metagenome-assembled genomes (MAGs) or any file with many short, unrelated sequences.
• Output files (downloadable after analysis):
  • GFF file with called genes.

Parameters

The values in brackets are the default ones:

• Workers [4]: integer 1–8; number of parallel web workers. Multiple input files are distributed across workers.
• Translation table [Default/Auto]: NCBI translation table (1–25, or 0 for auto-detection). See the official NCBI list for more information.
• Use metagenomic mode [false]: see General considerations above.
• Ignore truncated genes [false]: suppress reporting of genes that run off the edge of a contig (open ends).
• Break calling on N subsequences [false]: do not bridge over runs of unknown (N) bases when predicting genes.
• Ignore Shine-Dalgarno sequences [false]: force the algorithm to not use Shine-Dalgarno ribosome-binding site signals in gene calling.

Example

The following data can be used to try out gene calling:

• Species: Klebsiella pneumoniae
• Assembly: GCA_004138665.1 (FASTA, gzipped) from ENA