Annotation of ribosomal RNA genes in metagenomic fragments

 Ying Huang

California Institute for Telecommunications and Information Technology

University of California San Diego

La Jolla, California, United States of America

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Ying Huang, Paul Gilna and Weizhong Li. " Identification of ribosomal RNA genes in metagenomic fragments". Bioinformatics (2009) 25:1338-1340

News! The updated method, Meta_RNA(H3), is now available at WebMGA: Metagenomic Analysis Web Service Collection.


1. Supplementary Materials in Our Paper.

This link provides two supplementary tables in our paper. S1: genome names used in the benchmark study; S2: false positive rates of our algorithm for different sequence length.

Supplementary File


2. Algorithm as a stand-alone application

Our algorithm is implemented in Python language, see readme.txt for usage instruction


Download here


3. Updated Package using HMMER 3.0b3

This is an updated version, Meta_RNA(H3), of our package using HMMER 3.0b3 for model search. In our benchmark study on metagenome and metatranscriptome datasets (following reference), the Meta_RNA(H3) could be 35~70 times faster compare to previous implementaion using HMMER 2.3.2, Meta_RNA(H2). The algorithm is still implemented in Python language, see readme_H3.txt for usage instruction

Updates: I've tested the scripts on the latest HMMER 3.0, and a new parameter "-p" was added to enable hmmsearch for multiple threads

Ying Huang, Weizhong Li, Patricia W. Finn and David L. Perkins. Ribosomal RNA identification in metagenomic and metatranscriptomic datasets. Submitted as a bookchapter.

readme_H3.txt (old file)

Download here (old file)


News: updated software package by Sitao Wu ( Oct. 21, 2011

Download here (new file)

readme_new.txt (new file)