Wikiomics:RNA homology search

Probabilistic methods (SCFG/CM and HMMs)

• Infernal is an implementation of covariance models (profile stochastic context-free grammars) for RNA sequence/structure analysis. The Rfam database is maintained using Infernal.
• ERPIN (Easy RNA Profile IdentificatioN) is an RNA motif search program developed by Daniel Gautheret and André Lambert
• HomoStRscan A program for discovering homologous RNAs in complete genomes by taking a single RNA sequence with its secondary structure.
• PHMMTS An implementation of "pair hidden Markov models on tree structures (PHMMTSs)".
• RaveNnA A software package for faster covariance models whilst provably sacrificing no accuracy for rigorous filtering. Also includes heuristic filters.
• RNACAD A stochastic context-free grammar(SCFG) RNA modeling package that accounts for both primary and secondary structure information. SCFGs are robust and allow arbitrary deviations from a pattern.
• RSmatch RNA Secondary Structure Matcher: provides four functions: (1) regular database search, (2) multiple structure alignment, (3) iterative database search, and (4) pairwise sequence alignment.

RNA descriptor methods

• HyPa A system for the declarative description and efficient search of hybrid patterns in large genomic data sets.
• MilPat Motifs and Inter-moLecular motifs searching tool using Constraints Solving Problems formAlism and solving Technique.
• GUUGle A utility for fast exact matching under RNA base pairing rules. GUUGle efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length.
• PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.
• RNABOB is an implementation of D. Gautheret's RNAMOT, but with a different underlying algorithm using a nondeterministic finite state machine with node rewriting rules.
• RNAMotif Construct descriptors based upon consensus models of structural RNAs, these can be used to scan data-bases for matches.
• RNAMST an efficient and flexible RNA Motif Search Tool for RNA structural homologs. RNAMST web server accepts four different kinds of input formats to facilitate user to describe a RNA structure easily.

Family specific searches

• ARAGORN A program to detect tRNA genes and tmRNA genes in nucleotide sequences.
• BRUCE A program for the detection of transfer-messenger RNA genes in nucleotide sequences
• [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve