The HMMER web server

Contents:

• Target databases
  • Sequence databases
  • Profile HMM databases
  • Search provenance
• Searches
  • Search query
  • Query examples
  • Default search parameters
    • phmmer
    • hmmscan
    • hmmsearch
    • jackhmmer
  • Databases
    • Sequence databases
    • HMM databases
  • Thresholds
    • Significance thresholds
    • Reporting thresholds
    • Gathering thresholds
• Advanced search options
  • Customisation of results
  • Pfam search
  • Filters
    • Bias composition
  • Gap penalties
    • Open
    • Extend
    • Scoring Matrix
  • Glossary
• Results
  • Score view
    • Sequence Matches
    • Jackhmmer iterations
    • Customisation of Results
    • Profile HMM Matches
    • Domain Graphic
    • Downloading
  • Taxonomy view
    • Tree Graphic
    • Species Distribution
  • Domain Architecture view
    • Domain Graphic (Query)
    • Domain Architecture list
• API
  • Introduction
    • API Documentation
    • Examples using curl
  • Available services
    • phmmer searches
    • hmmscan searches
    • hmmsearch searches
    • jackhmmer searches
    • Results
    • Taxonomy and domain views
    • Batch searches
• About HMMER
  • HMMER project
  • Sponsors
  • How to cite
• The HMMER software
  • HMMER algorithms
  • Other programs
• Help
  • Helpdesk
  • Staying informed
• Appendices
  • Appendix A - Result object format
    • “Results” hash
    • “Stats” hash
    • “Sequence” hash
    • “Domain” Hash
  • Appendix B - response codes
  • Appendix C - data formats
  • Appendix D - unsupported features
  • Appendix E - Job ID
  • Appendix F - JSON format
• Changelog