(principles, help)

Easy identification of Rho–independent transcription terminators

Insert sequence data

Paste one or more nucleic acid sequences in FASTA format (max 5Mb):
>gi

Select options

Search strand:
Both
Forward
Reverse

Color terminator stem and loop:
Yes
No

Inverse U and T – select whether or not you want to keep Us (or Ts) as in input sequence or change them to Ts (or Us):
Keep
Change

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Principles

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.

To provide a uniform scoring scheme for Erpin and RNAmotif hits, we compute the free energy of the predicted terminator stem-loop structure using RNAfold (Hofacker et al. 1994). This free energy value may be used as a confidence value for predicted terminators.

User's Manual

Input sequences to be analyzed in the text area or upload from a local file. DNA or RNA sequences are accepted. Format is Fasta.
Options:

• 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.

Submit request using the ’Run’ button.
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)

References

• 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).

Credits

• Magali Naville
• Antonin Marchais
• Adrien Gilhot Gaudeffroy