SSU-ALIGN: structural alignment of SSU rRNA sequences

Overview

SSU-ALIGN is a software package for identifying, aligning, masking and visualizing archaeal 16S, bacterial 16S and eukaryotic 18S small subunit ribosomal RNA (SSU rRNA) sequences. It includes and uses the Infernal software package for generating alignments based on the conserved secondary structure and sequence of SSU rRNA. SSU-ALIGN extends Infernal to make it easier for users to generate large-scale alignments of up to millions of SSU rRNA sequences that will ultimately be used as input to phylogenetic inference methods. (SSU-ALIGN is not capable of inferring phylogenetic trees itself.) Large SSU rRNA sequence datasets are commonly generated by environmental sequencing survey studies that use SSU rRNA as a phylogenetic marker of species in the environment being studied. While designed primarily for these SSU-based studies, SSU-ALIGN is a general tool that can be used to generate alignments of any type of structural RNA, including large subunit ribosomal RNA (LSU rRNA).

The latest release of SSU-ALIGN is 0.1.1 [23 Feb 2016].

The 0.1.1 release is a very minor update to version 0.1. See the v0.1.1 release notes for more information.

Documentation:

• User's Guide [PDF, 101 pages].
• README from the current release.

Reference:

• The recommended citation for using SSU-ALIGN is E. P. Nawrocki, Structural RNA Homology Search and Alignment using Covariance Models, Ph.D. thesis, Washington University in Saint Louis, School of Medicine, (2009).

Download:

• The current source code distribution: SSU-ALIGN 0.1.1 [tarball, 19 MB]
  SSU-ALIGN is freely available under the Berkeley Software Distribution license [BSD].

We welcome code contributions, feature requests, and bug reports.

Note on SSU-ALIGN and Infernal 1.1

The latest release of SSU-ALIGN (version 0.1.1) includes a version of Infernal similar to Infernal version 1.0.2. It does not include or use the latest version of Infernal (version 1.1), which is significantly faster than 1.0.2 for RNA homology search. In terms of alignment speed, however, Infernal versions 1.1 and 1.0.2 are comparable, so updating SSU-ALIGN to use Infernal 1.1 would not have a dramatic effect on running time. Our plan is to eventually update SSU-ALIGN to use Infernal 1.1, but we don't have a planned timeframe for that update.

Further reference:

• Version 1.0 of Infernal is described in (Nawrocki, Kolbe, and Eddy, 2009).
• The Comparative RNA Website (CRW), the source of the sequence and structural data underlying SSU-ALIGN's SSU rRNA models, is described in (Cannone et al., 2002).
• A chapter of Biological Sequence Analysis (Durbin et al., 1998) describes covariance models, the profile probabilistic models used by SSU-ALIGN and Infernal, in more detail.
• Covariance models were originally described in (Eddy and Durbin, 1994). They were first implemented in the COVE software package.
• For additional references on CMs see the Infernal website.