Abstract

We present here a new approach to the problem of defining RNA signatures and finding their occurrences in sequence databases. The proposed method is based on “secondary structure profiles”. An RNA sequence alignment with secondary structure information is used as an input. Two types of weight matrices/profiles are constructed from this alignment: single strands are represented by a classical lod-scores profile while helical regions are represented by an extended “helical profile” comprising 16 lod-scores per position, one for each of the 16 possible base-pairs. Database searches are then conducted using a simultaneous search for helical profiles and dynamic programming alignment of single strand profiles. The algorithm has been implemented into a new software, ERPIN, that performs both profile construction and database search. Applications are presented for several RNA motifs. The automated use of sequence information in both single-stranded and helical regions yields better sensitivity/specificity ratios than descriptor-based programs. Furthermore, since the translation of alignments into profiles is straightforward with ERPIN, iterative searches can easily be conducted to enrich collections of homologous RNAs.

Author Keywords: RNA motifs; sequence alignment; secondary structure; motif search; profiles

Article Outline

• Introduction

• Results and discussion

• Secondary structure profiles and the ERPIN algorithm

• tRNA loops

• 23 S rRNA 301–337 region (L24 binding)

• Selenocysteine insertion sequence

• Iterative search: iron response elements

• Conclusion

• Materials and methods

• Single-strand profiles

• Helix profiles

• The ERPIN program

• Training sets

• Acknowledgements

• References

Corresponding author

¹ Edited by J. Doudna