RNAstructure GUI Help
Sequence File Formats: FASTA and SEQ
Nucleotide Sequences can be provided to RNAstructure in either FASTA or SEQ format.
In FASTA files, each nucleotide sequence begins with a single-line description that must start with the greater-than symbol (>). Subsequent lines should only contain the sequence itself. The sequence may be formatted with whitespace, which is ignored, however blank lines are not allowed in the middle of FASTA input. FASTA files should have a ".fasta" extension.
SEQ files have the following format:
Important notes regarding sequences in RNAstructure:
A CT (Connectivity Table) file contains secondary structure information for a sequence. These files are saved with a CT extension. When entering a structure to calculate the free energy, the following format must be followed.
The CT file may hold multiple structures for a single sequence. This is done by repeating the format for each structure without any blank lines between structures.
The CT file format is such that any files generated by RNAstructure are compatible with mfold/Unafold (available from Michael Zuker), and many other software packages.
Folding constraints are saved in plain text with a CON extension. These can be hand edited. For multiple entries of a specific type of constraint, entries are each listed on a separate line. When there is no constraint of a type, there are no lines required. Note that all specifiers, followed by "-1" or "-1 -1", are expected by RNAstructure. For all specifiers that take two arguments, it is assumed that the first argument is the lower base pair number. The file format is as follows:
The file format for SHAPE reactivity comprises two columns. The first column is the nucleotide number, and the second is the reactivity.
Nucleotides for which there is no SHAPE data can either be left out of the file, or the reactivity can be entered as less than -500. Columns are separated by any white space.
Note that there is no header information. Nucleotides 1 through 10 have no reactivity information. Nucleotide 11 has a normalized SHAPE reactivity of 0.042816. Nucleotide 12 has a normalized SHAPE reactivity of 0, which is NOT the same as having no reactivity when using the pseudo-energy constraints.
By default, RNAstructure looks for SHAPE data files to have the file extension SHAPE, but any plain text file can be read.
List files have a LIS extension. This file contains any number of sequences of any length or nucleic acid, each on its own line.
Alignment File Format
Alignment files are plain text. They are formatted as a nucleotide in the first sequence immediately followed by the nucleotide in the second sequence it's aligned to, separated by a space. Only one alignment pair can be on each line, and the last line of the file must be "-1 -1".
Visit The Mathews Lab RNAstructure Page for updates and latest information.