Conserved RNA structures (CRSs) in cyanobacteria

This web resource presents candidates for novel predicted conserved RNA structures (novel CRSs) and known RNA structures inside intergenic regions flanking 931 orthologous protein-coding gene groups in 202 cyanobacteria species-representative genomes from the proGenomes database.

This large-scale, phylum-wide comparative genomics study screens the intergenic regions located adjacent up-/downstream of orthologous genes for

1. bacterial known RNA structure families provided in Rfam database and bacterial transcription terminators by homology search using Infernal cmsearch, and
   
2. novel CRSs using the CMfinder tool and the local phylogeny of the orthologous genes.

The novel CRSs are characterized by

• structure covariation (determined with the R-scape tool) and sequence conservation of the post-processed structure alignment,
  
• putative cis-acting function through guilt by association to the annotated pathways of adjacent orthologous genes, and
  
• transcriptional activity based on >400 processed public single-end RNA-seq libraries from 9 genomes (using the the zFPKM method).

Counts of novel CRSs and their characterizations

Category	Candidate RNA structures	Associated with pathways	Transcriptionally active	Transcriptionally active in ≥ 2 genomes
High covariation	117	79	56	21
High sequence conservation	222	139	131	50
High power	70	37	57	36
In total	409	255	244	107

Click Browse CRSs to get started with exploring the novel CRSs.
Click Known structures to explore the Rfam hits and transcription terminators inside the intergenic search regions of this computational screen.

The data can also be downloaded as flat files:

• List of genomic locations and taxonomy of the novel CRSs
  
• List of all novel CRSs and their associated pathways
• Archive of the STOCKHOLM format alignments of all novel CRSs
• Archive of the Covariance Models of all novel CRSs
• List of Rfam families in the 202 genomes
• List of terminator sequences in the 202 genomes

If you use this resource, please cite:

Exploring the RNA structure regulatory potential in 202 cyanobacterial genomes
Adrian Sven Geissler, Elena Carrasquer-Alvarez, Christian Anthon, Niels-Ulrik Frigaard, Jan Gorodkin, and Stefan Ernst Seemann
submitted