ArticleNucleic acids research2013
TIGRFAMs and Genome Properties in 2013.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 374 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
374 citing papers in PubMed, 618 citations in OpenAlex.
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- Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes.Nature communications · 2026Article
- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
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- Complete genome sequence of Sphingomonas sp. gentR, a high-level gentamicin-resistant bacterium.Scientific data · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- 35 metagenomic datasets from the northern and southern parts of the Yap trench sediments.Scientific data · 2026Article
- Genomic and in vitro characterization of two lytic bacteriophages infecting multidrug-resistant Erwinia sp. strain AnSW2-5.Scientific reports · 2026Article
- Planococcus Daihaiensis sp. nov. Isolated from the Lake Water in Daihai.Current microbiology · 2026Article
- Comparative Genomic and Transcriptomic Analysis Reveals Why Paenarthrobacter Strains Are Specialists in the Degradation of the Fungicide Iprodione.Microbial biotechnology · 2026Article
- Metagenomic Identification and Characterization of Novel Vitamin BMicroorganisms · 2025Article
- Expanded gut microbial genomes from Chinese populations reveal population-specific genomic features related to human physiological traits.Genome medicine · 2025Article
- Potential for aerobic hydrocarbon oxidation in archaea.Nature communications · 2025Article
- Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution.Molecular ecology resources · 2025Article
- Electron shuttling promotes denitrification and mitigates nitrous oxide emissions in lakes.Nature communications · 2025Article
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- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
314 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
TIGRFAMs, available online at http://www.jcvi.org/tigrfams is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing more functionally heterogeneous families are designated subfamily or domain, and assign less specific but more widely applicable annotations. The Genome Properties database, available at http://www.jcvi.org/genome-properties, specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. TIGRFAMs and Genome Properties content are developed in concert because subsystems reconstruction for large numbers of genomes guides selection of seed alignment sequences and cutoff values during protein family construction. Both databases specialize heavily in bacterial and archaeal subsystems. At present, 4284 models appear in TIGRFAMs, while 628 systems are described by Genome Properties. Content derives both from subsystem discovery work and from biocuration of the scientific literature.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.