Annotation of
ribosomal RNA genes in metagenomic fragments
Ying
Huang
California
Institute for Telecommunications and Information Technology
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._________________________________________________
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.
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2. Algorithm as a stand-alone
application
Our
algorithm is implemented in Python language, see readme.txt for usage instruction
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.
Download here (old file)
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Download here (new file)