SSU-ALIGN(1)

NAME
SSU-ALIGN(package) - alignment, masking and visualization of SSU rRNA sequences

SYNOPSIS
ssu-align
  Align small subunit ribosomal RNA (16S/18S SSU rRNA) sequences ssu-build
  Build SSU rRNA covariance models from multiple sequence alignment(s) ssu-draw
  Draw secondary structure diagrams of SSU rRNA ssu-mask
  Mask (remove columns from) SSU rRNA multiple sequence alignments ssu-merge
  Merge SSU rRNA alignments created by parallel ssu-align jobs ssu-prep
  Prepare SSU rRNA sequences for parallel ssu-align jobs

DESCRIPTION

SSU-ALIGN is a suite of several programs for creating, masking and visualizing small subunit ribosomal RNA (SSU rRNA) multiple sequence alignments. It uses profile probabilistic models called "profile hidden Markov models" (profile HMMs) and "covariance models" (CMs) that represent archaeal 16S SSU rRNA, bacterial 16S SSU rRNA and eukaryotic 18S SSU rRNA. Each of these profile models was built from a reference alignment derived from Robin Gutell's Comparative RNA Website database (CRW) (Cannone et al., BMC Bionformatics. 2002; 3:2.) as described in the user's guide. The alignments created by SSU-ALIGN explicitly take into account the conserved secondary structure of SSU as annotated by CRW. SSU-ALIGN output alignments are created at a rate of roughly one sequence per second for full length SSU sequences.

The main program, ssu-align takes a FASTA-formatted sequence file containing SSU sequences, classifies them by domain of life (i.e. archaea, bacteria, or eukarya) and creates structurally annotated domain-specific alignments.

ssu-mask removes columns from (masks) alignments created by ssu-align that are likely to contain alignment errors. The set of columns to remove is determined based on per-nucleotide confidence estimates (posterior probabilities, annotated in 'PP' lines) contained within the alignments as calculated by ssu-align. Alternatively, preset masks can be applied to remove a consistent set of columns to allow comparison across multiple datasets. ssu-mask can also be used to convert alignments to aligned FASTA and to remove a subset of sequences from an alignment.

The ssu-draw program generates secondary structure diagrams of SSU in postscript or PDF format from ssu-align generated alignments. (PDF is possible only if a postscript to pdf converter like 'ps2pdf' is in your PATH). Diagrams of individual aligned sequences or alignment summary statistics can be generated.

The ssu-prep program can be used for splitting up large sequence files into many smaller ones to be aligned separately in parallel on a cluster or multi-core machine. It outputs a shell script that will execute the set of parallel ssu-align jobs and then automatically merge their results. The final alignments will be identical to what would have been created by a single ssu-align job that processed the full original sequence file.

ssu-merge merges the results of a set of parallel ssu-align jobs created by ssu-prep. It is automatically called by the final ssu-align job of the set, and so should only be necessary to be called manually on the command-line in the event that one or more of the jobs fail. If this happens, only the failed jobs need be rerun, and then the full set can be merged by executing ssu-merge.

Finally, ssu-build constructs new profile models (CMs) from input structurally annotated alignments. These can either be full length or partial SSU models. For example, models that represent only hypervariable region V4 can be constructed for aligning datasets from a PCR-based study that targetted the V4 region.

SSU-ALIGN is designed to be able to create and manipulate very large alignments (up to millions of sequences). The main limitation for large alignments is the time required to create them (about 1 sequence/second/cpu). The memory requirements of SSU-ALIGN are effectively independent of the number of sequences in the alignments.

Each of the six programs has its own man page.

The SSU-ALIGN programs internally execute programs from the INFERNAL package and the Easel sequence analysis library. INFERNAL is developed by Eric Nawrocki, Diana Kolbe, and Sean Eddy. Easel is developed by Sean Eddy. The INFERNAL and Easel programs installed with SSU-ALIGN include a ssu- prefix to distinguish them from separate installations of INFERNAL and/or Easel that may be on your system. For example, the cmsearch INFERNAL program used by SSU-ALIGN is called ssu-cmsearch. Each of these programs has its own man page as well.