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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)
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.
- Colorstock: ANSI terminal color
SScolor and SScolorMult
- SScolor: static HTML
- Download the script: sscolor.pl
- 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
- Documentation is available by typing perldoc sscolorMult.pl or sscolorMult.pl -h
- The perldoc for sscolor.pl contains the full documentation
- 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
- XREI -- an XRATE grammar and alignment browser
-- Ian Holmes - 23 Oct 2007