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Seed 1.0


This web site contains the source code for the software system Seed. This computer program takes as input a set of unaligned RNA sequences and produces a set of secondary structure motifs. Suffix arrays are used enumerate complementary regions, possibly containing interior loops, as well for matching RNA secondary structure expressions.


Seed was developed at the University of Ottawa by Truong Nguyen under the supervision of Marcel Turcotte.


The project is documented by the following publications.
  1. Mohammad Anwar and Marcel Turcotte (Accepted) An approach to selecting putative RNA motifs using MDL principle. BIOCOMP'06 - The 2006 International Conference on Bioinformatics & Computational Biology, pages 560-565, Las Vegas, Nevada, USA, June 26-29, 2006.
    [ Paper ]

  2. Mohammad Anwar and Marcel Turcotte (Accepted) Evaluation of RNA secondary structure motifs using regression analysis. Canadian Conference on Electrical and Computer Engineering 2006, pages 1716-1721, Ottawa, Canada, May 7-10 2006.
    [ Paper ]

  3. Mohammad Anwar, Truong Nguyen and Marcel Turcotte (2006) Identification of consensus RNA secondary structures using suffix arrays. BMC Bioinformatics, 7:244
    [ Paper ]


  4. Truong Nguyen and Marcel Turcotte (2005) Exploring the Space of RNA Secondary Structure Motifs Using Suffix Arrays. 6th International Symposium on Computational Biology and Genome Informatics (CBGI 2005). Editors S. Blair et al., Salt Lake City, Utah, USA, July 21-26, 2005, 1291--1298.
    [ Paper | Slides ]

  5. Mohammad Anwar (2006) . Implementation and evaluation of scoring schemes for the automated discovery of nucleic acid structures. Master of Science, University of Ottawa.

  6. Truong Nguyen (2004) Efficient Determination of Concensus Secondary Structures in RNA. Master of Applied Science in Electrical Engineering, University of Ottawa.


Download: seed.tar.gz