ArticleNucleic acids research2010
Ab initio gene identification in metagenomic sequences.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 891 papers.
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Who cites it
891 citing papers in PubMed, 1,886 citations in OpenAlex.
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- Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.International journal of molecular sciences · 2026Article
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- Camel Milk Alleviates Chronic Fatigue Syndrome-like Symptoms in Mice by Modulating the Small Intestinal Microbiota and Inflammation.Foods (Basel, Switzerland) · 2026Article
- Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.medRxiv : the preprint server for health sciences · 2026Article
- Limosilactobacillus reuteri LR-99 Modulates Gut Microbiota and Core Symptoms in Children with Autism Spectrum Disorder: A Single-arm Pilot Study.Probiotics and antimicrobial proteins · 2026Article
- Linoleic acid enhances ruminal carbohydrate metabolism and biohydrogenation to promote rumen epithelial development in calves.NPJ biofilms and microbiomes · 2026Article
- Comparative Analysis of Microbial Community Structure and Functional Traits of Baijiu Daqu Across Diverse Geographical Regions in China.Foods (Basel, Switzerland) · 2026Article
- Preoperative gut microbial network alterations and BCAA-Related metabolic disturbance in postoperative delirium after cardiac surgery: a prospective matched multi-omic study.Translational psychiatry · 2026Article
- Metagenomic Insights into Gut Microbiota Alterations FollowingInternational journal of molecular sciences · 2026Article
831 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
3 authors at 1 institution in 1 country.
Funding
Abstract
We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed to bypass this difficulty, one effective method is to estimate parameters from dependencies, formed in evolution, between frequencies of oligonucleotides in protein-coding regions and genome nucleotide composition. Original version of the method was proposed in 1999 and has been used since for (i) reconstructing codon frequency vector needed for gene finding in viral genomes and (ii) initializing parameters of self-training gene finding algorithms. With advent of new prokaryotic genomes en masse it became possible to enhance the original approach by using direct polynomial and logistic approximations of oligonucleotide frequencies, as well as by separating models for bacteria and archaea. These advances have increased the accuracy of model reconstruction and, subsequently, gene prediction. We describe the refined method and assess its accuracy on known prokaryotic genomes split into short sequences. Also, we show that as a result of application of the new method, several thousands of new genes could be added to existing annotations of several human and mouse gut metagenomes.
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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.