README

Seed - library and tools to explore RNA secondary structure motifs space using enhanced suffix arrays
Truong Nguyen and Marcel Turcotte (C) 2003-18 University of Ottawa

Contact:

Marcel Turcotte
School of Electrical Engineering and Computer Science (EECS)
University of Ottawa
800 King Edward
Ottawa, Ontario, K1N 6N5
Canada

marcel.turcotte@uottawa.ca

bio.site.uottawa.ca/software/seed

References:

 @article{985389,
    author = {Mohamed Ibrahim Abouelhoda and Stefan Kurtz and Enno Ohlebusch},
    title = {Replacing suffix trees with enhanced suffix arrays},
    journal = {J. of Discrete Algorithms},
    volume = {2},
    number = {1},
    year = {2004},
    issn = {1570-8667},
    pages = {53--86},	
    doi = {http://dx.doi.org/10.1016/S1570-8667(03)00065-0},
    publisher = {Elsevier Science Publishers B. V.},
    address = {Amsterdam, The Netherlands, The Netherlands}
 }
 
 @InProceedings{Karkkainen2003,
     author =	 {K\"arkk\"ainen, Juha and Sanders, Peter},
     title =	 {Simple Linear Work Suffix Array Construction},
     booktitle = {Annual Symposium on Combinatorial Pattern Matching},
     pages =	 {943--955},
     year =	 2003,
     volume =	 2719,
     series =	 {Lecture Notes in Computer Science},
     address =	 {Berlin},
     publisher = {Springer-Verlag},
     note = {\url{http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2719&spage=943}}
 }
  
 @InProceedings{Kasai2001,
     author =	 {Kasai, Toru and Lee, Gunho and Arimura, Hiroki and
                 Arikawa, Setsuo and Park, Kunsoo},
     title =	 {Linear-Time Longest-Common-Prefix Computation in
                 Suffix Arrays and Its Applications},
     booktitle = {Annual Symposium on Combinatorial Pattern Matching},
     pages =	 {181--192},
     year =	 2001,
     volume =	 2089,
     series =	 {Lecture Notes in Computer Science},
     address =	 {Berline},
     publisher = {Springer-Verlag},
     note =      {\url{http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2089&spage=181}}
 }