Jul 20, 2023

Python binding for Prodigal, an ORF finder for genomes and metagenomes

Pyrodigal is a Python module that provides bindings to Prodigal using Cython.

Features The library now features everything from the original Prodigal CLI

  • run mode selection Choose between single mode, using a training sequence to count nucleotide hexamers, or metagenomic mode, using pre-trained data from different organisms prodigal -p.
  • region masking Prevent genes from being predicted across regions containing unknown nucleotides prodigal -m.
  • closed ends Genes will be identified as running over edges if they are larger than a certain size, but this can be disabled prodigal -c.
  • training configuration During the training process, a custom translation table can be given prodigal -g, and the Shine-Dalgarno motif search can be forcefully bypassed prodigal -n
  • output files Output files can be written in a format mostly compatible with the Prodigal binary, including the protein translations in FASTA format prodigal -a, the gene sequences in FASTA format prodigal -d, or the potential gene scores in tabular format prodigal -s.

Checkout these related ports:
  • Wise - Intelligent algorithms for DNA searches
  • Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
  • Vt - Discovers short variants from Next Generation Sequencing data
  • Vsearch - Versatile open-source tool for metagenomics
  • Viennarna - Alignment tools for the structural analysis of RNA
  • Velvet - Sequence assembler for very short reads
  • Vcftools - Tools for working with VCF genomics files
  • Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
  • Vcf2hap - Generate .hap file from VCF for haplohseq
  • Vcf-split - Split a multi-sample VCF into single-sample VCFs
  • Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
  • Unanimity - Pacific Biosciences consensus library and applications
  • Ugene - Integrated bioinformatics toolkit
  • Ucsc-userapps - Command line tools from the UCSC Genome Browser project
  • Trimmomatic - Flexible read trimming tool for Illumina NGS data