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MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction

Gang-Qing Hu, Jiang-Tao Guo, Yong-Chu Liu, Huaiqiu Zhu
2009 Computer applications in the biosciences : CABIOS  
The method employs a two-step strategy to predict translation initiation sites (TISs) by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each  ...  We proposed a tool named MetaTISA with an aim to improve TIS prediction of current gene-finders for metagenomes.  ...  ACKNOWLEDGEMENTS We are grateful to Dr Hideki Noguchi from Mitsubishi Research Institute and Ms Katharina J. Hoff from University of Goettingen for useful email communications.  ... 
doi:10.1093/bioinformatics/btp272 pmid:19389734 fatcat:eehtkvqvbffy5fp4af6i6fdtly

Gene prediction in metagenomic fragments: A large scale machine learning approach

Katharina J Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, Peter Meinicke
2008 BMC Bioinformatics  
Additionally, this method is able to predict translation initiation sites accurately and distinguishes complete from incomplete genes with high reliability.  ...  In the first stage, we use linear discriminants for monocodon usage, dicodon usage and translation initiation sites to extract features from DNA sequences.  ...  In addition, we provide a detailed analysis of the translation initiation site (TIS) prediction performance and we also investigate the ability to discriminate between complete and incomplete genes.  ... 
doi:10.1186/1471-2105-9-217 pmid:18442389 pmcid:PMC2409338 fatcat:f63d4jpihndutayeoqpyui5o6e

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering

David R. Kelley, Bo Liu, Arthur L. Delcher, Mihai Pop, Steven L. Salzberg
2011 Nucleic Acids Research  
In a comparison among multiple gene finding methods, Glimmer-MG makes the most sensitive and precise predictions on simulated and real metagenomes for all read lengths and error rates tested.  ...  In this work, we developed a metagenomics gene prediction system Glimmer-MG that achieves significantly greater accuracy than previous systems via novel approaches to a number of important prediction subtasks  ...  ACKNOWLEDGEMENTS We thank Derrick Wood for helpful TIS discussion and manuscript comments.  ... 
doi:10.1093/nar/gkr1067 pmid:22102569 pmcid:PMC3245904 fatcat:evg4llnbzjbtjcqxpiooidldky

Orphelia: predicting genes in metagenomic sequencing reads

Katharina J. Hoff, Thomas Lingner, Peter Meinicke, Maike Tech
2009 Nucleic Acids Research  
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  ...  Metagenomic sequencing projects yield numerous sequencing reads of a diverse range of uncultivated and mostly yet unknown microorganisms.  ...  We thank Dr Mario Stanke for discussions about the evaluation of gene predictions on the hypersaline microbial mat data set.  ... 
doi:10.1093/nar/gkp327 pmid:19429689 pmcid:PMC2703946 fatcat:kladqrtgqvh55l6ddt4mxwyz4e

Gene prediction in metagenomic fragments based on the SVM algorithm

Yongchu Liu, Jiangtao Guo, Huaiqiu Zhu
2011 2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)  
Then, proteincoding sequences are identified for each group independently with SVM classifiers that integrate entropy density profiles (EDP) of codon usage, translation initiation site (TIS) scores and  ...  Results: In this article, we present a novel gene prediction method named MetaGUN for metagenomic fragments based on a machine learning approach of SVM.  ...  Xuegong Zhang of Tsinghua University for interest to the project and useful discussions. We also thank Dr.  ... 
doi:10.1109/bmei.2011.6098588 dblp:conf/bmei/LiuGZ11 fatcat:lsjyts6i5fdfjpwxm5kq3wby6e

Gene prediction in metagenomic fragments based on the SVM algorithm

Yongchu Liu, Jiangtao Guo, Gangqing Hu, Huaiqiu Zhu
2013 BMC Bioinformatics  
Then, proteincoding sequences are identified for each group independently with SVM classifiers that integrate entropy density profiles (EDP) of codon usage, translation initiation site (TIS) scores and  ...  Results: In this article, we present a novel gene prediction method named MetaGUN for metagenomic fragments based on a machine learning approach of SVM.  ...  Xuegong Zhang of Tsinghua University for interest to the project and useful discussions. We also thank Dr.  ... 
doi:10.1186/1471-2105-14-s5-s12 pmid:23735199 pmcid:PMC3622649 fatcat:tp5w47gy25azfagxxfldffgroa

GeneMark-HM: improving gene prediction in DNA sequences of human microbiome

Alexandre Lomsadze, Christophe Bonny, Francesco Strozzi, Mark Borodovsky
2021 NAR Genomics and Bioinformatics  
Tests of GeneMark-HM on simulated metagenomes demonstrated improvement in gene annotation of human metagenomic sequences in comparison with the current state-of-the-art gene prediction tools.  ...  We have shown that reconstructed prokaryotic genomes along with genomes of sequenced microbial isolates can be used to support more accurate gene prediction in novel metagenomic sequences.  ...  The authors have no conflicts of interest to declare aside from the fact that several of the authors are employees of private companies, Gene Probe, Inc. and Enterome, as stated in the title page of the  ... 
doi:10.1093/nargab/lqab047 pmid:34056597 pmcid:PMC8153819 fatcat:riddm5hcmzejrllmlkr5jqt6fq

An Alternative Platform for Protein Expression Using an Innate Whole Expression Module from Metagenomic DNA

Dae-Eun Cheong, So-Youn Park, Ho-Dong Lim, Geun-Joong Kim
2019 Microorganisms  
by plentiful cis-acting elements in the spanning regions around the ORF such as the promoter, ribosome binding site (RBS), terminator, and 3′-/5′-UTRs for gene expression.  ...  For a proof-of-principle study, we mined a complete expression module with an innately overexpressed ORF in E. coli from a metagenomics DNA library, and incorporated it into a vector that had no regulatory  ...  Prediction of Translation Initiation Rate of Foreign ORFs in the pBEM Series Vector To validate the effects of the leader sequence on the translation of foreign genes, we predicted the translation initiation  ... 
doi:10.3390/microorganisms7010009 pmid:30626052 pmcid:PMC6352095 fatcat:ardxemvdsbf2pbokfuhtekhaau

Detection of Novel Integrons in the Metagenome of Human Saliva

Supathep Tansirichaiya, Md. Ajijur Rahman, Agata Antepowicz, Peter Mullany, Adam P. Roberts, Axel Cloeckaert
2016 PLoS ONE  
In this work, a PCR-based approach was used to investigate the presence of integrons and associated gene cassettes in human oral metagenomic DNA obtained from both the UK and Bangladesh.  ...  We identified a diverse array of gene cassettes containing ORFs predicted to confer antimicrobial resistance and other adaptive traits.  ...  We thank Prof Pål Johnsen of UiT The Arctic University of Norway for helpful comments and suggestions on the initial version of the manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0157605 pmid:27304457 pmcid:PMC4909258 fatcat:piqaqix7tvdevfvcd3y4ggy32i

Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover

Christopher Staley, Trevor J. Gould, Ping Wang, Jane Phillips, James B. Cotner, Michael J. Sadowsky
2014 Frontiers in Microbiology  
Discrepancies between metagenomic and PICRUSt taxonomic-functional relationships, however, suggested potential functional redundancy among abundant and rare taxa that impeded the ability to accurately  ...  assess unique functional traits among rare taxa at this sequencing depth.  ...  while at the same time predicting many genes not found in metagenomic data.  ... 
doi:10.3389/fmicb.2014.00414 pmid:25152748 pmcid:PMC4126211 fatcat:7vr3b77btrg7dlcpy2kicm7oti

Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

Disa Bäckström, Natalya Yutin, Steffen L. Jørgensen, Jennah Dharamshi, Felix Homa, Katarzyna Zaremba-Niedwiedzka, Anja Spang, Yuri I. Wolf, Eugene V. Koonin, Thijs J. G. Ettema, Richard P. Novick
2019 mBio  
Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth  ...  Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments.  ...  Identification of viral metagenomic sequences. Protein sequences of the metagenomic contigs were predicted using Prodigal v.2.6.3 (96) in the metagenomics mode.  ... 
doi:10.1128/mbio.02497-18 pmid:30837339 pmcid:PMC6401483 fatcat:r3fiyozhjnfd3a3m45jrs5f7lm

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

Natalya Yutin, Kira S. Makarova, Ayal B. Gussow, Mart Krupovic, Anca Segall, Robert A. Edwards, Eugene V. Koonin
2017 Nature Microbiology  
Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and  ...  and predict the functions of the majority of phage proteins, in particular, those that comprise the structural, replication and expression modules.  ...  Wolf and Sergey Shmakov for invaluable technical help, and Koonin group members for helpful discussion.  ... 
doi:10.1038/s41564-017-0053-y pmid:29133882 pmcid:PMC5736458 fatcat:32i3y5sidzchha2irgibdhinma

Characterization of the SOS meta-regulon in the human gut microbiome

Joseph P. Cornish, Neus Sanchez-Alberola, Patrick K. O'Neill, Ronald O'Keefe, Jameel Gheba, Ivan Erill
2014 Computer applications in the biosciences : CABIOS  
transcriptional repressor to sites in the promoter of a cell wall biogenesis enzyme, a phage integrase and a death-on-curing protein.  ...  We predict the association of this network with three novel protein clusters involved in cell wall biogenesis, chromosome partitioning and restriction modification, and we confirm binding of the SOS response  ...  All identified LexA-binding sites were associated with the predicted protein-coding gene in the metagenome sequence whose translational start site was closest to the LexA-binding site.  ... 
doi:10.1093/bioinformatics/btt753 pmid:24407225 pmcid:PMC3998124 fatcat:5m5ijazb3rfkte64fpcdiwg5cq

[PROVISIONAL] Boundaries in metagenomic screenings using lacZα-based vectors

Luana de Fátima Alves, Tiago Cabral Borelli, Cauã Antunes Westmann, Rafael Silva-Rocha, María-Eugenia Guazzaroni
2019 Genetics and Molecular Biology  
, but rather due to the insertion of small metagenomic DNA fragments in frame within the coding region of the lacZ gene present in the original vector.  ...  As these vectors are massively used in functional metagenomic screenings, we highlight the importance of reporting boundaries in established metagenomic screenings methodologies.  ...  that reduced mRNAs stability near the translation-initiation site had increased protein expression(Kudla et al. 2009;Gu et al. 2010;Goodman metagenomic library for proteases may lead to false positives  ... 
doi:10.1590/1678-4685-gmb-2018-0252 pmid:31429862 pmcid:PMC7198016 fatcat:q3wriyfimfesxlmqyajo3q4psu

geneRFinder: gene finding in distinct metagenomic data complexities

Raíssa Silva, Kleber Padovani, Fabiana Góes, Ronnie Alves
2021 BMC Bioinformatics  
Conclusions We provide geneRFinder, an approach for gene prediction in distinct metagenomic complexities, available at gitlab.com/r.lorenna/generfinder and https://osf.io/w2yd6/, and also we provide a  ...  Average prediction rates of geneRFinder differed in percentage terms by 54% and 64%, respectively, against Prodigal and FragGeneScan while handling high complexity metagenomes.  ...  Availability and requirements Project name: geneRFinder; Project home page: gitlab.com/r.lorenna/generfinder and https ://osf.io/w2yd6 /; Operating system(s): Platform independent; Programming language  ... 
doi:10.1186/s12859-021-03997-w pmid:33632132 fatcat:cy27hd6w5zf5zku5yvrqm2wxuy
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