Variants

Supplementary online files: Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

The following data files are supplementary to the paper “Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity”. They are stored within four Zip-file archives. The first three archive files store alignments, and in these files, each alignment is stored in Stockholm format, which can be display using many text editors such as Emacs on UNIX or Microsoft Word. The alignment files can also be interpreted by many programs, such as those in Infernal.

• File 1: Alignments of variant riboswitches predicted in the work. Key nucleotides are indicated by a ‘X’ symbol within the #=GC CORE line. The key nucleotides within the relevant group(s) are given in the #=GF CORESEQ line.
• File 2: Additional alignments of known riboswitch classes. The purpose of these alignments is described in the legend to supplementary Table S1. Included are .cm files, which can be used with the cmsearch program within Infernal version 1.1
• File 3: This file contains the alignments of all groups of all riboswitches that were analyzed in this work. Other data on these alignments is in the next archive
• File 4: This files contains information on all riboswitch groups analyzed in this work. The archive consists of two files that are tables stored in HTML format. The first file is called ligand-changes-groups.html and contains these columns: “friendlyName” (a human-readable name describing the analyzed RNA), “rnaName” (the Rfam accession, or a reference to the additional alignments with .cm files mentioned above), “pdbId” (the accession of the crystal structure used from PDB), “chain” (the chain that was analyzed in the PDB entry), “coreDist” (the distance used to define key nucleotides), “isCrystal” (whether the group contains the sequence that was crystallized), “projSeq” (the identities of the key nucleotides for the given group), “redundant with” (indicates which groups have the same key nucleotides as other groups, and are therefore redundant; note that adenine and guanine riboswitches come from the same purine riboswitch alignment, and many adenine groups are identical to guanine groups), “pvaluesiter0” (the two p-values for the motif before the homology search), “iter0motif” (a link to the alignment for this motif before homology search; note that the link will only work if the alignments are unzipped into the same directory), “pvaluesiter1” (the two p-values for the motif after the automated homology search, if the search was performed on the group), “iter1motif” (link to the alignment for the motif after the automated homology search, if one was performed on the group). The second file is called ligand-changes-genes.html. Its columns are: “motif” (the motif identifier, which refers to the iter0motif or iter1motif fields in ligand-changes-groups.html), “cddname” (the accession for the relevant conserved domain in the Conserved Domain Database, version 2.25), “freq” (the frequency with which genes with this domain are regulated by riboswitches in the given group).