Abstract
Metagenomic and metatranscriptomic shotgun sequencing techniques are gaining popularity as more cost-effective
next-generation sequencing technologies become commercially available. The initial stage of bioinformatic
analysis generally involves the identification of phylogenetic markers such as ribosomal RNA genes.
The sequencing reads that do not code for rRNA can then be used for protein-based analysis. Hidden Markov
model is a well-known method for pattern recognition. Hidden Markov models that are trained on well-curated
rRNA sequence databases have been successfully used to identify DNA sequence coding for rRNAs in prokaryotes.
Here, we introduce rRNASelector, which is a computer program for selecting rRNA genes from
massive metagenomic and metatranscriptomic sequences using hidden Markov models. The program successfully
identified prokaryotic 5S, 26S, and 23S rRNA genes from Roche 454 FLX Titanium-based metagenomic and
metatranscriptomic libraries. The rRNASelector program is available at http://sw.ezbiocloud.net/rrnaselector.
Citations
Citations to this article as recorded by
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives
Jammi Prasanthi Sirasani, Cory Gardner, Gihwan Jung, Hyunju Lee, Tae-Hyuk Ahn
Briefings in Bioinformatics.2025;[Epub] CrossRef - Bioinformatic approaches for studying the microbiome of fermented food
Liam H. Walsh, Mairéad Coakley, Aaron M. Walsh, Paul W. O’Toole, Paul D. Cotter
Critical Reviews in Microbiology.2023; 49(6): 693. CrossRef - Methods included
Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, The CWL Community
Communications of the ACM.2022; 65(6): 54. CrossRef - Rapid and accurate identification of ribosomal RNA sequences via deep learning
Zhi-Luo Deng, Philipp C Münch, René Mreches, Alice C McHardy
Nucleic Acids Research.2022; 50(10): e60. CrossRef - Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation
Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch-Mizrachi, Eric P. Nawrocki
BMC Bioinformatics.2021;[Epub] CrossRef - VADR: validation and annotation of virus sequence submissions to GenBank
Alejandro A. Schäffer, Eneida L. Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi, Eric P. Nawrocki
BMC Bioinformatics.2020;[Epub] CrossRef - Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species
Marko Verce, Luc De Vuyst, Stefan Weckx
Frontiers in Microbiology.2019;[Epub] CrossRef - Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment
Lee J. Pinnell, Jeffrey W. Turner
Frontiers in Microbiology.2019;[Epub] CrossRef - Gene‐Centric Metagenome Analysis Reveals Gene Clusters for Carbon Monoxide Conversion and Validates Isolation of a Clostridial Acetogen for C2 Chemical Production
Hyunsoo Kang, Byeonghyeok Park, Nicole R. Bolo, Duleepa Pathiraja, Shinyoung Park, Minseok Cha, In‐G. Choi, In S. Chang
Biotechnology Journal.2019;[Epub] CrossRef - Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp
Juseok Kim, Joon Yong Kim, Hye Seon Song, In-Tae Cha, Seong Woon Roh, Se Hee Lee
Journal of Microbiology.2019; 57(6): 444. CrossRef - Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data
Sohyun Bang, DongAhn Yoo, Soo-Jin Kim, Soyun Jhang, Seoae Cho, Heebal Kim
Scientific Reports.2019;[Epub] CrossRef - A strong link between marine microbial community composition and function challenges the idea of functional redundancy
Pierre E Galand, Olivier Pereira, Corentin Hochart, Jean Christophe Auguet, Didier Debroas
The ISME Journal.2018; 12(10): 2470. CrossRef - Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities
Fabien Cottier, Kandhadayar Gopalan Srinivasan, Marina Yurieva, Webber Liao, Michael Poidinger, Francesca Zolezzi, Norman Pavelka
npj Biofilms and Microbiomes.2018;[Epub] CrossRef - EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
Alex L Mitchell, Maxim Scheremetjew, Hubert Denise, Simon Potter, Aleksandra Tarkowska, Matloob Qureshi, Gustavo A Salazar, Sebastien Pesseat, Miguel A Boland, Fiona M I Hunter, Petra ten Hoopen, Blaise Alako, Clara Amid, Darren J Wilkinson, Thomas P Curt
Nucleic Acids Research.2018; 46(D1): D726. CrossRef - ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services
Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen
F1000Research.2017; 6: 70. CrossRef - RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
Chao Xie, Chin Lui Wesley Goi, Daniel H. Huson, Peter F. R. Little, Rohan B. H. Williams
BMC Bioinformatics.2016;[Epub] CrossRef - An evaluation of the accuracy and speed of metagenome analysis tools
Stinus Lindgreen, Karen L. Adair, Paul P. Gardner
Scientific Reports.2016;[Epub] CrossRef - Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes
Jiarong Guo, James R. Cole, Qingpeng Zhang, C. Titus Brown, James M. Tiedje, P. D. Schloss
Applied and Environmental Microbiology.2016; 82(1): 157. CrossRef - riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics
Matteo Ramazzotti, Luisa Berná, Claudio Donati, Duccio Cavalieri
Frontiers in Genetics.2015;[Epub] CrossRef - Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces
SangJoon Mo, Bong-Soo Kim, Sung-Jo Yun, Jung-Ju Lee, Suk-Hyun Yoon, Chung-Hun Oh
Gut Pathogens.2015;[Epub] CrossRef - Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies
Anastasis Oulas, Christina Pavloudi, Paraskevi Polymenakou, Georgios A. Pavlopoulos, Nikolas Papanikolaou, Georgios Kotoulas, Christos Arvanitidis, loannis Iliopoulos
Bioinformatics and Biology Insights.2015; 9: BBI.S12462. CrossRef - Genome sequence of type strain of Staphylococcus aureus subsp. aureus
Bong-Soo Kim, Hana Yi, Jongsik Chun, Chang-Jun Cha
Gut Pathogens.2014;[Epub] CrossRef - EBI metagenomics—a new resource for the analysis and archiving of metagenomic data
Sarah Hunter, Matthew Corbett, Hubert Denise, Matthew Fraser, Alejandra Gonzalez-Beltran, Christopher Hunter, Philip Jones, Rasko Leinonen, Craig McAnulla, Eamonn Maguire, John Maslen, Alex Mitchell, Gift Nuka, Arnaud Oisel, Sebastien Pesseat, Rajesh Radh
Nucleic Acids Research.2014; 42(D1): D600. CrossRef - Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms
Shana K Goffredi, Hana Yi, Qingpeng Zhang, Jane E Klann, Isabelle A Struve, Robert C Vrijenhoek, C Titus Brown
The ISME Journal.2014; 8(4): 908. CrossRef - Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
Mincheol Kim, Hyun-Seok Oh, Sang-Cheol Park, Jongsik Chun
International Journal of Systematic and Evolutionary Microbiology
.2014; 64(Pt_2): 346. CrossRef - SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
Evguenia Kopylova, Laurent Noé, Hélène Touzet
Bioinformatics.2012; 28(24): 3211. CrossRef - Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
Ok-Sun Kim, Yong-Joon Cho, Kihyun Lee, Seok-Hwan Yoon, Mincheol Kim, Hyunsoo Na, Sang-Cheol Park, Yoon Seong Jeon, Jae-Hak Lee, Hana Yi, Sungho Won, Jongsik Chun
International Journal of Systematic and Evolutionary Microbiology
.2012; 62(Pt_3): 716. CrossRef - Draft Genome Sequence of Staphylococcus saprophyticus subsp. saprophyticus M1-1, Isolated from the Gills of a Korean Rockfish, Sebastes schlegeli Hilgendorf, after High Hydrostatic Pressure Processing
Bong-Soo Kim, Chong-Tai Kim, Bang Heon Park, Sujin Kwon, Yong-Jin Cho, Namsoo Kim, Chul-Jin Kim, Jongsik Chun, Jangyul Kwak, Jin-Soo Maeng
Journal of Bacteriology.2012; 194(16): 4441. CrossRef - Identification and removal of ribosomal RNA sequences from metatranscriptomes
Robert Schmieder, Yan Wei Lim, Robert Edwards
Bioinformatics.2012; 28(3): 433. CrossRef
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