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Updated: May 16, 2026
09:10
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
TIGRFAMs and Genome Properties in 2013.
Daniel H Haft1, Jeremy D Selengut, Roland A Richter
1Informatics, J Craig Venter Institute, Rockville, MD 20850, USA. haft@jcvi.org
Nucleic Acids Research
|December 1, 2012
Summary
TIGRFAMs is a protein family database using hidden Markov models (HMMs) for automated protein annotation. It works with Genome Properties to reconstruct microbial subsystems, aiding in genome analysis.
Area of Science:
- Genomics
- Bioinformatics
- Proteomics
Background:
- TIGRFAMs is a protein family database providing HMMs, seed alignments, and cutoff scores for automated protein annotation.
- The Genome Properties database aids in reconstructing molecular subsystems within genomes using evidence, including TIGRFAMs HMM results.
- Both databases focus on bacterial and archaeal subsystems, with TIGRFAMs containing 4284 models and Genome Properties describing 628 systems.
Purpose of the Study:
- To describe the TIGRFAMs database of protein family definitions and its integration with the Genome Properties database.
- To explain the development process and content of TIGRFAMs and Genome Properties, emphasizing their collaborative nature.
- To highlight the utility of these databases for microbial subsystem reconstruction and genome annotation.
Main Methods:
- Development of hidden Markov models (HMMs) from seed alignments of representative protein sequences.
- Application of cutoff scores for automated annotation pipelines to identify protein family members.
- Integration of TIGRFAMs HMM results within the Genome Properties database for subsystem reconstruction.
Main Results:
- TIGRFAMs currently comprises 4284 protein family models.
- Genome Properties describes 628 molecular subsystems.
- Content is derived from subsystem discovery and biocuration of scientific literature.
Conclusions:
- TIGRFAMs and Genome Properties are valuable, integrated resources for microbial genomics and bioinformatics.
- The collaborative development ensures that subsystem reconstruction informs protein family model refinement.
- These databases are essential tools for annotating proteins and understanding functional systems in bacteria and archaea.
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