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

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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, 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

readme_H3.txt

Download here