ArticleDatabase : the journal of biological databases and curation2012
AntiFam: a tool to help identify spurious ORFs in protein annotation.
Article in Database : the journal of biological databases and curation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 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
48 citing papers in PubMed.
- Sialidase inhibitor modulates gut microbiota and enhances mucosal protection in the treatment of ulcerative colitis.mSystems · 2026Trial
- "Quadrupling" the protein family space with global metagenomics.Nucleic acids research · 2026Article
- Antisense transcription reveals disease-associated adaptations in the human gut microbiome.Nature microbiology · 2026Article
- Current advances in psittacine beak and feather disease: From molecular pathogenesis to integrated surveillance and global control strategies.Veterinary world · 2026Review
- Draft genome ofMicrobiology resource announcements · 2026Article
- Testing the reliability of AI-generated protein structures.bioRxiv : the preprint server for biology · 2026Article
- High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.Nature communications · 2026Article
- Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling.Nature microbiology · 2026Article
- Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- A multi-Omic resource for exploring microbial eukaryotes in the meromictic freshwater Lake Pavin.Scientific data · 2026Article
- Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins.Bioinformatics advances · 2026Article
- Comprehensive multi omics explore the microbial function in metabolic pathway flow during altered diet.NPJ science of food · 2025Article
- Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes.Microbiome · 2025Article
- sORFdb - a database for sORFs, small proteins, and small protein families in bacteria.BMC genomics · 2025Article
- mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies.Bioinformatics (Oxford, England) · 2025Article
- InterPro: the protein sequence classification resource in 2025.Nucleic acids research · 2025Article
- Comprehensive Analysis of Vaginal and Gut Microbiome Alterations in Endometriosis Patients.International journal of women's health · 2025Article
- Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations.Communications biology · 2024Article
- Article
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.
Funding
Abstract
As the deluge of genomic DNA sequence grows the fraction of protein sequences that have been manually curated falls. In turn, as the number of laboratories with the ability to sequence genomes in a high-throughput manner grows, the informatics capability of those labs to accurately identify and annotate all genes within a genome may often be lacking. These issues have led to fears about transitive annotation errors making sequence databases less reliable. During the lifetime of the Pfam protein families database a number of protein families have been built, which were later identified as composed solely of spurious open reading frames (ORFs) either on the opposite strand or in a different, overlapping reading frame with respect to the true protein-coding or non-coding RNA gene. These families were deleted and are no longer available in Pfam. However, we realized that these may perform a useful function to identify new spurious ORFs. We have collected these families together in AntiFam along with additional custom-made families of spurious ORFs. This resource currently contains 23 families that identified 1310 spurious proteins in UniProtKB and a further 4119 spurious proteins in a collection of metagenomic sequences. UniProt has adopted AntiFam as a part of the UniProtKB quality control process and will investigate these spurious proteins for exclusion.
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.