Pathway Tools File Formats

Input File Formats for Building New Pathway/Genome Databases

Overall we recommend GFF3 format because a single GFF3 file can contain all sequence plus annotation for a genome with multiple replicons, and because we have observed problems with representation of alternative splicing in GenBank-format files.

• Input and output format: Sample GFF3 Format file
  • One .gbff file can contain all sequence plus annotation for multiple replicons (.gbk files cannot contain multiple replicons)
  • Better representation of alternative splicing than RefSeq .gbk files
  • Producers of GFF3 files that are known to work with Pathway Tools:
    • RefSeq prokaryotic and eukaryotic files
    • NCBI Prokaryotic Annotation Pipeline

• Input and output format: Sample GenBank Format file
  • One .gbff file can contain all sequence plus annotation for multiple replicons (.gbk files cannot contain multiple replicons)
  • Sometimes representation of alternative splicing is problematic
  • Producers of GenBank files that are known to work with Pathway Tools:
    • RefSeq prokaryotic and eukaryotic files
    • NCBI Prokaryotic Annotation Pipeline
    • Prokka
    • RAST

• Input format: Sample PathoLogic Format file
  • Separate files required for each replicon
  • Separate files required for sequence
  • Best for simple genomes with a single replicon
  • Cannot represent alternative splicing
  • Requires a separate genetic-elements.dat file to list annotation and sequence files for each replicon: Sample genetic-elements.dat file

Other Input File Formats

• Input format: SBML format
• Input format: BioPAX format

Input File Formats

• Output format: Flatfile format for Pathway/Genome DBs