HMMER web server
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Target databases
Searches
Advanced search options
Results
API
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The HMMER software
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The HMMER web server
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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
Gene3D and Superfamily thresholds
Advanced search options
Taxonomy Restrictions
Search
Pre-defined Taxonomic Tree
Customisation of results
Pfam search
Filters
Bias composition
Gap penalties
Open
Extend
Scoring Matrix
Batch searches
Glossary
Results
Score view
Sequence Matches
Jackhmmer iterations
Customisation of Results
Profile HMM Matches
Domain Graphic
Other Sequence Features
Downloading
Search details
Taxonomy view
Tree Graphic
Species Distribution
Downloading
Search details
Domain Architecture view
Domain Graphic (Query)
Domain Architecture list
Downloading
Search details
API
Introduction
Using curl
Using a script
Retrieving results
Available services
phmmer searches
hmmscan searches
hmmsearch searches
jackhmmer searches
Taxonomic restrictions
Annotation searches
Results
Deleting results
Taxonomy and domain views
Examples
phmmer
hmmscan
jackhmmer
Batch searches
Fetching results
Downloading files from 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
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