(principles, help)Easy identification of Rho–independent transcription terminators
ARNold finds rho-independent terminators in nucleic acid sequences. The search procedure uses two complementary programs, Erpin and RNAmotif.
- Erpin (Gautheret & Lambert, 2001) is given a structure-annotated alignment of 1200 terminator sequences from Bacillus subtilis and Escherichia coli as a training set. It builds a lod-score profile from this alignment and seeks high scoring instances of the profile in the user's sequence.
- RNAmotif (Macke et al. 2001) uses a descriptor developed by Lesnik et al. (2001) to recognize E. coli terminators, however it can be applied to find terminators from any species. Essentially, the descriptor consists of a 4-18 bp helix, a 0-2 nt spacer and a 12 nt T-rich region. RNAmotif matches are scored using the sequence contents of the T-rich region and stability of the stem loop region and an emprirical score cutoff is defined to accept or reject matches.
Input sequences to be analyzed in the text area or upload from a local file.
DNA or RNA sequences are accepted. Format is Fasta.
- Search strand: perform analysis on forward, reverse, or both strands.
- Colored secondary structures: transforms the parenthesis in colored secondary structures, where loops are in this color and stems in this one.
- Inverse U and T: keeps U/T as in input, or reverse.
Results are displayed in a single page, with the following information given for each predicted terminator:
- 5' end position of predicted transcription terminator (for terminators on minus strand, position is given in plus strand coordinates, end of terminator first).
- Program that produced prediction
- Strand (+/-)
- Sequence (parenthesis or colors indicate terminator stem). Lowercase letters in RNAmotif predictions indicate the spacer element, between the stem-loop and T-rich region.
- Free energy of stem-loop region (kcal/mol)
- Gautheret D, Lambert A. (2001) Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles. J Mol Biol. 313:1003–11 (abstract).
- Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M and Schuster P. (1994) Fast Folding and comparison of RNA secondary structures. Monastch. Chem., 125:167-188 (abstract).
- Lesnik EA et al. (2001) Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Research, 29: 3583-3594.
- Macke T, Ecker D, Gutell R, Gautheret D, Case DA and Sampath R. (2001) RNAMotif – A new RNA secondary structure definition and discovery algorithm. Nucleic Acids Res. 29:4724–4735 (abstract).
- Magali Naville
- Antonin Marchais
- Adrien Gilhot Gaudeffroy