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

My Email: yih007@ucsd.edu

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.

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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

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2. Algorithm as a stand-alone application

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

readme.txt

Download here

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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)

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News: updated software package by Sitao Wu (siw006.AT.ucsd.edu) Oct. 21, 2011

Download here (new file)

readme_new.txt (new file)