Stemloc
Encyclopedia
Stemloc is a program for pairwise RNA structural alignment based on probabilistic models of RNA structure
known as Pair stochastic context-free grammars
. Stemloc implements constrained versions of the Sankoff algorithms for simultaneous structure prediction and sequence alignment of multiple RNAs.
Stemloc can be downloaded as part of the DART software package. It accepts input files in either FASTA
or Stockholm format
.
RNA structure
Biomolecular structure is the structure of biomolecules, mainly proteins and the nucleic acids DNA and RNA. The structure of these molecules is frequently decomposed into primary structure, secondary structure, tertiary structure, and quaternary structure. The scaffold for this structure is...
known as Pair stochastic context-free grammars
Stochastic context-free grammar
A stochastic context-free grammar is a context-free grammar in which each production is augmented with a probability...
. Stemloc implements constrained versions of the Sankoff algorithms for simultaneous structure prediction and sequence alignment of multiple RNAs.
Stemloc can be downloaded as part of the DART software package. It accepts input files in either FASTA
FASTA format
In bioinformatics, FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences...
or Stockholm format
Stockholm format
Stockholm format is a Multiple sequence alignment format used by Pfam and Rfam to disseminate protein and RNA sequence alignments. The alignment editors...
.