ribosomal RNA genes in metagenomic fragments
California Institute for Telecommunications and Information Technology
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Ying Huang, Paul Gilna and Weizhong Li. " Identification of ribosomal RNA genes in metagenomic fragments". Bioinformatics (2009) 25:1338-1340News! 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.
2. Algorithm as a stand-alone application
Our algorithm is implemented in Python language, see readme.txt for usage instruction
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.
Download here (old file)
_________________________________________________News: updated software package by Sitao Wu (siw006.AT.ucsd.edu) Oct. 21, 2011
Download here (new file)