RNA Alignment Viewers

This page gives details of how to access three RNA alignment viewer tools described in the following paper

• Bendana YR, Holmes IH.  Colorstock, SScolor, Raton: RNA Alignment Visualization Tools.  Bioinformatics. 2008 Jan 24;. (pdf)

The three tools use three different rendering technologies (ANSI terminal color, static HTML generation & javascript) to address the same visualization task (colorizing RNA multiple alignments by secondary structure and highlighting compensatory mutations).

• RNA Alignment Viewers
• Input format
  • Example alignment files
• Tools
  • Colorstock
  • SScolor and SScolorMult
  • Raton
• Related Links

Input format

All three tools require the input alignments to be in Stockholm format.

Example alignment files

Here are a few examples of Stockholm-format alignment files to get you started:

• Coronavirus SL-III cis-acting replication element
• Coronavirus 3'UTR pseudoknot -- the example used in the screenshots below.
  • Note that the pseudoknotted parts of the secondary structure (labeled with A and a in the SS_cons line) are not colored as base-pairs by these tools
• let7 microRNA
• Hammerhead ribozyme (type I)

All of these examples are from RFAM. You can find many more alignments there.

Tools

Colorstock

• Colorstock: ANSI terminal color
  • Download the script: colorstock.pl
    • Also distributed as part of DART
    • See also Stockholm Tools
  • Documentation is available by typing perldoc colorstock.pl or colorstock.pl -h
    • The latter is a brief help message; the perldoc contains the full documentation

Colorstock screenshot:

SScolor and SScolorMult

• SScolor: static HTML
  • Download the script: sscolor.pl
    • sscolorMult.pl requires the Perl module Stockholm.pm in the PERL5LIB include path
    • Also distributed, with dependencies, as part of DART
    • See also Stockholm Tools
  • Documentation is available by typing perldoc sscolor.pl or sscolor.pl -h
    • The latter is a brief help message; the perldoc contains the full documentation

• SScolorMult: uses SScolor to generate a family of interlinked HTML pages, one for each possible reference sequence in an alignment
  • Download the script: sscolorMult.pl
    • Requires the Perl module Stockholm.pm which must be in the PERL5LIB include path
    • Also distributed, with dependencies, as part of DART
    • See also Stockholm Tools
  • Documentation is available by typing perldoc sscolorMult.pl or sscolorMult.pl -h
    • The perldoc for sscolor.pl contains the full documentation

SScolor screenshot:

Raton

• Raton: javascript / dynamic HTML
  • See RATON for description, access instructions, URL of prototype & how to install a local copy
  • Note that there is a prototype linked to from that page

Raton screenshot:

Related Links

• XREI -- an XRATE grammar and alignment browser

-- IanHolmes - 23 Oct 2007