Journal of Mathematical Biology

, Volume 56, Issue 1–2, pp 201–214 | Cite as

PSSMTS: position specific scoring matrices on tree structures



Identifying non-coding RNA regions on the genome using computational methods is currently receiving a lot of attention. In general, it is essentially more difficult than the problem of detecting protein-coding genes because non-coding RNA regions have only weak statistical signals. On the other hand, most functional RNA families have conserved sequences and secondary structures which are characteristic of their molecular function in a cell. These are known as sequence motifs and consensus structures, respectively. In this paper, we propose an improved method which extends a pairwise structural alignment method for RNA sequences to handle position specific scoring matrices and hence to incorporate motifs into structural alignment of RNA sequences. To model sequence motifs, we employ position specific scoring matrices (PSSMs). Experimental results show that PSSMs enable us to find individual RNA families efficiently, especially if we have biological knowledge such as sequence motifs.


Structural alignment Position specific scoring matrix Non-coding RNA 

Mathematics Subject Classification (2000)



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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Kengo Sato
    • 1
  • Kensuke Morita
    • 2
  • Yasubumi Sakakibara
    • 2
  1. 1.Japan Biological Informatics ConsortiumTokyoJapan
  2. 2.Department of Biosciences and InformaticsKeio UniversityYokohamaJapan

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