Computational and experimental identification of C. elegans microRNAs by comparative genomics

Yonatan Grad1,2, John Kim1,3, John Aach1,2, Gabriel D. Hayes1,3, George M. Church2, and Gary Ruvkun3

1These authors contributed equally to this work.

2The Lipper Center for Computational Genetics, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

3Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02114, USA

Correspondence should be addressed to G.R. (e-mail:

Supplemental materials


  1. Abstract
  2. Methods
  3. Obtaining the srnaloop program
  4. Supplementary Tables and Figures
  5. Further Assistance
  6. Copyright


MicroRNAs (miRNAs) constitute an extensive class of non-coding RNAs that are thought to regulate the expression of target genes via complementary base-pair interactions. To date, biochemical cloning has identified ~200 miRNAs from diverse eukaryotic organisms. Despite its success, such biochemical approaches are skewed towards identifying abundant miRNAs, unlike genome-wide, sequence-based computational predictions. We developed informatic methods to predict miRNAs in the C. elegans genome using sequence conservation and structural similarity to known miRNAs and generated 214 candidates. We confirmed the expression of four new miRNAs by Northern blotting and used a more sensitive PCR approach to verify the expression of many more candidates. Based on hypotheses underlying our computational methods, we estimate that the C. elegans genome may encode up to ~850 miRNAs.


Methods may be viewed here.

Obtaining the srnaloop program

Source code that can be compiled under UNIX and executable are available here.

To compile the source code for UNIX, use the following command:

gcc -lm -o srnaloop srnaloop.c 

Help may be obtained by running srnaloop with no parameters.

Note 08/04/2004:As of today a new version (1.02) of srnaloop is provided that contains a fix for a segmentation fault on program termination. Thanks go to Iosif Nietzke of the Danforth Center for alerting us to the problem.

Supplementary Tables and Figures

Supplementary Figure 1

Supplementary Table I

Supplementary Table II



Copyright (c) 2003 by John Aach and the President and Fellows of Harvard University

All other material

Copyright (c) 2003 by Yonatan Grad, John Aach, and the President and Fellows of Harvard University

Further Assistance

Contact Yonatan Grad or John Aach for further assistance on the computation aspects of this study or this website, and John Kim on the experimental aspects of this study.

This page last updated by JA on 4 Aug 2004.