| Title |
NOTE] rRNASelector: A Computer Program for Selecting Ribosomal RNA Encoding Sequences from Metagenomic and Metatranscriptomic Shotgun Libraries |
| Author |
Jae-Hak Lee1, Hana Yi2, and Jongsik Chun1,2,3* |
| Address |
1Interdisciplinary Graduate Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea, 2Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Republic of Korea, 3School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea |
| Bibliography |
Journal of Microbiology, 49(4),689-691, 2011,
|
| DOI |
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| Key Words |
rRNASelector, metagenomics, metatranscriptomics, HMMER, rRNA, computer program |
| 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. |
