R2R: publication-quality drawings of RNAs
The purpose of R2R is to allow the user to make aesthetically pleasing, high-quality drawings of RNA secondary structures. A particular focus of the software is on consensus diagrams of conserved RNAs.
CMfinder: inference and scoring of conserved RNA secondary structures
This software package includes three programs: CMfinder, RNAphylo and hmmpair. CMfinder is a method to find and align a conserved RNA secondary structure using unaligned sequences as input. The input sequences can include extraneous sequences or subsequences. RNAphylo and hmmpair are two different algorithms to score the structural alignments that are the output of CMfinder. The software package also includes a method to combine the results of RNAphylo and hmmpair into a unified score.
Paper (which presented an earlier version of the software): https://www.ncbi.nlm.nih.gov/pubmed/16357030
Paper (which presented an updated software version): https://academic.oup.com/nar/article/45/18/10811/4080188
Source code: https://sourceforge.net/projects/weinberg-cmfinder/
overcluster2: clustering of subsequences based on sequence homology
This software is used when there are a large set of non-coding sequences (e.g., inter-genic regions) that might contain conserved motifs. After running all-against-all comparisons with BLAST, overcluster2 can be used to cluster subsequences. It is important to cluster subsequences (instead of complete sequences, as with programs like blastclust), because each individual input sequence might contain multiple functional elements.
Repository of RNA multiple-sequence alignments
This is a bitbucket repository of all multiple-sequence alignments of conserved structured RNAs arising from our work (including work done while in Ron Breaker’s lab). It includes experimentally confirmed RNAs and predicted RNAs.