ArticleBMC bioinformatics2023
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 14 citations in OpenAlex.
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- Cancer epitope prediction tools and analysis pipelines in CEDAR.Nucleic acids research · 2026Article
- Comprehensive mapping of identical sequences across human proteins emphasizes the widespread issue of shared epitopes in self-antigens.NAR genomics and bioinformatics · 2026Article
- Curation at Scale with EPITOME: Extraction Pipeline for Immunological Texts and Open-Source Multimodal Enquiry.bioRxiv : the preprint server for biology · 2026Article
- The immunogenicity database collaborative: a standardized, publicly available database for clinical immunogenicity observations and insights.Frontiers in immunology · 2026Article
- The Cancer Epitope Database and Analysis Resource (CEDAR): current capabilities and future directions.Frontiers in oncology · 2026Review
- Immunoinformatics-based design of a multi-epitope mRNA vaccine candidate targeting the major human-infecting hepatitis E virus genotypes 1-4.Frontiers in bioinformatics · 2026Article
- Rational discovery of peptide inhibitors targeting Keap1: a focus on neurodegenerative diseases.Frontiers in bioinformatics · 2026Article
- Designing a multi-epitope mRNA vaccine to combat human metapneumovirus based on consensus sequence using reverse vaccinology.Journal of computer-aided molecular design · 2025Article
- A single point mutation on FLT3L-Fc protein increases the risk of immunogenicity.Frontiers in immunology · 2025Article
- Identification of natural Zika virus peptides presented on the surface of paediatric brain tumour cells by HLA class I.PloS one · 2025Article
- Distinct Omicron longitudinal memory T cell profile and T cell receptor repertoire associated with COVID-19 hospitalisation.Frontiers in immunology · 2025Article
- Next-generation IEDB tools: a platform for epitope prediction and analysis.Nucleic acids research · 2024Article
- Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgGmAbsArticle
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Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundNumerous tools exist for biological sequence comparisons and search. One case of particular interest for immunologists is finding matches for linear peptide T cell epitopes, typically between 8 and 15 residues in length, in a large set of protein sequences. Both to find exact matches or matches that account for residue substitutions. The utility of such tools is critical in applications ranging from identifying conservation across viral epitopes, identifying putative epitope targets for allergens, and finding matches for cancer-associated neoepitopes to examine the role of tolerance in tumor recognition.
resultsWe defined a set of benchmarks that reflect the different practical applications of short peptide sequence matching. We evaluated a suite of existing methods for speed and recall and developed a new tool, PEPMatch. The tool uses a deterministic k-mer mapping algorithm that preprocesses proteomes before searching, achieving a 50-fold increase in speed over methods such as the Basic Local Alignment Search Tool (BLAST) without compromising recall. PEPMatch's code and benchmark datasets are publicly available.
conclusionsPEPMatch offers significant speed and recall advantages for peptide sequence matching. While it is of immediate utility for immunologists, the developed benchmarking framework also provides a standard against which future tools can be evaluated for improvements. The tool is available at https://nextgen-tools.iedb.org , and the source code can be found at https://github.com/IEDB/PEPMatch .
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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.