ArticleNucleic acids research2009
Orphelia: predicting genes in metagenomic sequencing reads.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Multi-feature fusion for gene prediction and functional peptide identification.Frontiers in microbiology · 2026Article
- IntegratedNAR genomics and bioinformatics · 2023Article
- A toolbox of machine learning software to support microbiome analysis.Frontiers in microbiology · 2023Review
- FragGeneScanRs: faster gene prediction for short reads.BMC bioinformatics · 2022Article
- geneRFinder: gene finding in distinct metagenomic data complexities.BMC bioinformatics · 2021Article
- NGS read classification using AI.PloS one · 2021Article
- Updated review of research on the gut microbiota and their relation to depression in animals and human beings.Molecular psychiatry · 2020Review
- PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning.Bioinformatics (Oxford, England) · 2020Article
- CNN-MGP: Convolutional Neural Networks for Metagenomics Gene Prediction.Interdisciplinary sciences, computational life sciences · 2019Article
- Article
- Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks.Frontiers in microbiology · 2019Review
- Conducting metagenomic studies in microbiology and clinical research.Applied microbiology and biotechnology · 2018Review
- Opportunities and obstacles for deep learning in biology and medicine.Journal of the Royal Society, Interface · 2018Review
- Feature selection for gene prediction in metagenomic fragments.BioData mining · 2018Article
- Composition Analysis and Feature Selection of the Oral Microbiota Associated with Periodontal Disease.BioMed research international · 2018Article
- A clinician's guide to microbiome analysis.Nature reviews. Gastroenterology & hepatology · 2017Review
- Gene Prediction in Metagenomic Fragments with Deep Learning.BioMed research international · 2017Article
- An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.Journal of proteome research · 2016Article
- HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.Frontiers in microbiology · 2016Article
- Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.Bioinformatics and biology insights · 2015Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomic sequencing projects yield numerous sequencing reads of a diverse range of uncultivated and mostly yet unknown microorganisms. In many cases, these sequencing reads cannot be assembled into longer contigs. Thus, gene prediction tools that were originally developed for whole-genome analysis are not suitable for processing metagenomes. Orphelia is a program for predicting genes in short DNA sequences that is available through a web server application (http://orphelia.gobics.de). Orphelia utilizes prediction models that were created with machine learning techniques on the basis of a wide range of annotated genomes. In contrast to other methods for metagenomic gene prediction, Orphelia has fragment length-specific prediction models for the two most popular sequencing techniques in metagenomics, chain termination sequencing and pyrosequencing. These models ensure highly specific gene predictions.
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Registered trials
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