Poster abstracts

Poster number 52 submitted by Robert Knarr

Using JAVA to find secondary structure motifs in bpseq files

Robert Knarr (Allegheny College), Dr. Martin Serra (Allegheny College)

Abstract:
Significant improvements were made on a JAVA program designed to search though bpseq files describing secondary structure (1). This program features a graphical user interface and allows the user to search bpseq files for various RNA secondary structural motifs. The search yields information about position and number of times the query appears in the user specified dataset. The improvements include providing a visualization of the query motif(2), and a more thorough exploration of the helical regions including predicted thermodynamics based on the helix sequence. These search results give insight as to what structures and sequences are prevalent in nature. We intend to use the results to gather statistical information about the stems surrounding various RNA secondary structural elements(3).

For instance after a search for all single nucleotide budges the resulting dataset was easily explored. The mean length for stems surrounding a single nucleotide was found to be 4 nucleotides with an average predicted Gibbs free energy of the stem of -6.20 kJ/mol. The average ratio of number of nucleotides in the longer stem to number of nucleotides in the shorter stem is 2.2:1, and the average ratio of the more stable to less stable stem free energy is 5.5:1.

References:
1 Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D\'Souza

L.M., Du Y., Feng B., Lin N., Madabusi L.V., MÜller K.M., Pande N.,
Shang Z., Yu N., and Gutell R.R. (2002). The Comparative RNA Web (CRW)
Site: An Online Database of Comparative Sequence and Structure
Information for Ribosomal, Intron, and Other RNAs. BioMed Central
Bioinformatics, 3:2.

2 Kévin Darty, Alain Denise, Yann Ponty

VARNA: Interactive drawing and editing of the RNA secondary structure.
Bioinformatics, pp. 1974-1975, Vol. 25, no. 15, 2009

3 Blose JM, Manni ML, Klapec KA, Stranger-Jones Y, Zyra AC, Sim V,

Griffith CA, Long JD, Serra MJ. Non-nearest-neighbor dependence of the
stability for RNA bulge loops based on the complete set of group I
single-nucleotide bulge loops. Biochemistry (2007) 46:15123–15135.

Keywords: BioInformatics, Secondary structure, JAVA search program