RNAAlignment Viewers

RNA Alignment Viewers

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

• Bendaña & Holmes: Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinformatics 2008;24:579-80. (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).

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:

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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:

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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:

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Related Links

• XREI -- an XRATE grammar and alignment browser

-- Ian Holmes - 23 Oct 2007