SSU-ALIGN: structural alignment of SSU rRNA sequences
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 [11 June 2010].
SSU-ALIGN tutorial in February 2013 in Austin, TX
Eric Nawrocki will be presenting a talk on profile-based multiple
alignment and a tutorial on SSU-ALIGN at the
Symposium and Workshop on New Methods for Phylogenomics and
Metagenomics at UT-Austin on Feb 17, 2013.
- A one-page summary of the tutorial, with a list of all commands used,
- What will be covered in the tutorial:
- We will use SSU-ALIGN to generate, mask and
visualize SSU alignments using a small, contrived SSU rRNA
example dataset (included in the SSU-ALIGN package).
The tutorial will orient users with the various programs
that make up SSU-ALIGN:
- ssu-align for identifying and aligning archaeal, bacterial and
eukaryotic SSU sequences in an input sequence file.
- ssu-mask for removing alignment columns with significant levels
of uncertainty (alignment masking), as preparation for later
- ssu-draw for visualizing alignment statistics and individual
sequences in the form of secondary structure diagrams.
- ssu-prep for faster alignment of large datasets through
parallelization on CPU-clusters. (The tutorial does not require
access to a cluster.)
- ssu-build for creating truncated models of a specific region of
SSU rRNA or new models of other structural RNAs for using with
- Software and system requirements for the tutorial:
- All of the software required software for running SSU-ALIGN comes
included with the package, which can be downloaded
here. Optionally, you can install the 'ps2pdf' program
which is part of Ghostscript, available for download from
- If you are using Mac OS/X, and you have not yet installed the
XCode developer tools, you must do so before the installation
instructions in the user guide will work. You can download
XCode from the Mac App store.
- SSU-ALIGN is designed to be built and used on UNIX platforms. It is
developed mainly on Intel GNU/Linux systems and Mac OS, and
has been tested on a variety of other UNIX platforms including:
Fedora, Debian, SUSE, OpenSUSE and Ubuntu.
- SSU-ALIGN is not currently tested on Microsoft Windows, but it may
work there. If you would like to use it on Windows, I recommend you
try to perform the installation using CYGWIN to see if will run on
- Preparing for the tutorial:
- Install SSU-ALIGN on the computer that you will bring to
the tutorial. Installation
instructions are available in chapter 2 of the
User's Guide. Optionally, you can download and install
Ghostscript, which includes the 'ps2pdf' program from
here. After downloading, unpack, configure, make and
install with the following commands: 'tar xfz
ghostscript-9.05.tgz', 'cd ghostscript-9.05', './configure', 'make',
'make install'. (If you have permission to install programs on
your machine, but 'make install' does not work, try 'sudo make install'.)
- If you're interested in background information on SSU-ALIGN, read through chapters 1-6 of the
- For even more background, take a look at the second half of my
Ph.D. thesis, which focuses on SSU-ALIGN. Chapter 7
discusses the historical relevance of SSU in phylogenetic
inference and explains the motivation for the development of
the software. For yet more information, see the
Further reference section below.
- The tutorial will include exercises very similar or identical to
those in the Tutorial section of the
User's Guide (chapter 4). You can go through it yourself in
preparation, or just wait until the Austin tutorial.
Note on SSU-ALIGN and Infernal 1.1
The latest release of SSU-ALIGN (version 0.1) includes a version of
Infernal much like 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 to SSU-ALIGN to use Infernal 1.1 would not have a dramatic
effect of running time. Our plan is to eventually update SSU-ALIGN to
use Infernal 1.1, but the exact timeframe for that update is currently
- 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
(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
- Covariance models were originally described in
(Eddy and Durbin, 1994). They were first implemented
COVE software package.
- For additional references on CMs see the
Last modified: Tue Dec 18 06:16:16 2012