Practical: Building covariance models

This section will walk you through building a covariance model from a single sequence and will give you practical experience using tools from the RNA folding and RNA homology lectures. It provides an introduction to methods that may be useful if you would like to submit your own RNA families to Rfam and/or the RNA Families Track at RNA Biology. This practical was created by Lars Barquist for courses run at the IGC in Oeiras, Portugal (2012) and the Cambridge Graduate School of Life Sciences. A preprint of a book chapter on this subject which covers much more background and theory is available on arXiv here.

This tutorial will walk you through identifying homologous sequences based on single sequence search; predicting alignments and structure; editing predictions; and constructing a covariance model and using it to search genomes of interest. The basic idea is to provide a "recipe" you can use to investigate your own RNA molecules of interest.

If you find the information on these pages useful in your research, please cite:

Barquist, L, Burge, SW, and Gardner, PP. Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. Curr Protoc Bioinformatics. 2016 Jun 20;54:12.13.1-12.13.25 (https://www.ncbi.nlm.nih.gov/pubmed/27322404)