Local Alignment of RNA Sequences with Arbitrary Scoring Schemes. Backofen, R., Hermelin, D., Landau, G. M., & Weimann, O. In Lewenstein, M. & Valiente, G., editors, Combinatorial Pattern Matching, 17th Annual Symposium, CPM 2006, Barcelona, Spain, July 5-7, 2006, Proceedings, volume 4009, of Lecture Notes in Computer Science, pages 246–257, 2006. Springer.
Local Alignment of RNA Sequences with Arbitrary Scoring Schemes [link]Paper  doi  bibtex   
@inproceedings{DBLP:conf/cpm/BackofenHLW06,
  author    = {Rolf Backofen and
               Danny Hermelin and
               Gad M. Landau and
               Oren Weimann},
  editor    = {Moshe Lewenstein and
               Gabriel Valiente},
  title     = {Local Alignment of {RNA} Sequences with Arbitrary Scoring Schemes},
  booktitle = {Combinatorial Pattern Matching, 17th Annual Symposium, {CPM} 2006,
               Barcelona, Spain, July 5-7, 2006, Proceedings},
  series    = {Lecture Notes in Computer Science},
  volume    = {4009},
  pages     = {246--257},
  publisher = {Springer},
  year      = {2006},
  url       = {https://doi.org/10.1007/11780441\_23},
  doi       = {10.1007/11780441\_23},
  timestamp = {Tue, 14 May 2019 10:00:38 +0200},
  biburl    = {https://dblp.org/rec/conf/cpm/BackofenHLW06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

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