MOTIVATION: The contig orientation problem, which we formally define as the MAX-DIR problem, has at times been addressed cursorily and at times using various heuristics. In setting forth a linear-time reduction from the MAX-CUT problem to the MAX-DIR problem, we prove the latter is NP-complete. We compare the relative performance of a novel greedy approach with several other heuristic solutions. RESULTS: Our results suggest that our greedy heuristic algorithm not only works well but also outperforms the other algorithms due to the nature of scaffold graphs. Our results also demonstrate a novel method for identifying inverted repeats and inversion variants, both of which contradict the basic single-orientation assumption. Such inversions have previously been noted as being difficult to detect and are directly involved in the genetic mechanisms of several diseases. AVAILABILITY AND IMPLEMENTATION: http://bioresearch.byu.edu/scaffoldscaffolder. CONTACT: paulmbodily@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: The contig orientation problem, which we formally define as the MAX-DIR problem, has at times been addressed cursorily and at times using various heuristics. In setting forth a linear-time reduction from the MAX-CUT problem to the MAX-DIR problem, we prove the latter is NP-complete. We compare the relative performance of a novel greedy approach with several other heuristic solutions. RESULTS: Our results suggest that our greedy heuristic algorithm not only works well but also outperforms the other algorithms due to the nature of scaffold graphs. Our results also demonstrate a novel method for identifying inverted repeats and inversion variants, both of which contradict the basic single-orientation assumption. Such inversions have previously been noted as being difficult to detect and are directly involved in the genetic mechanisms of several diseases. AVAILABILITY AND IMPLEMENTATION: http://bioresearch.byu.edu/scaffoldscaffolder. CONTACT: paulmbodily@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Serafim Batzoglou; David B Jaffe; Ken Stanley; Jonathan Butler; Sante Gnerre; Evan Mauceli; Bonnie Berger; Jill P Mesirov; Eric S Lander Journal: Genome Res Date: 2002-01 Impact factor: 9.043
Authors: Jonathan Butler; Iain MacCallum; Michael Kleber; Ilya A Shlyakhter; Matthew K Belmonte; Eric S Lander; Chad Nusbaum; David B Jaffe Journal: Genome Res Date: 2008-03-13 Impact factor: 9.043
Authors: Michael C Zody; Zhaoshi Jiang; Hon-Chung Fung; Francesca Antonacci; LaDeana W Hillier; Maria Francesca Cardone; Tina A Graves; Jeffrey M Kidd; Ze Cheng; Amr Abouelleil; Lin Chen; John Wallis; Jarret Glasscock; Richard K Wilson; Amy Denise Reily; Jaime Duckworth; Mario Ventura; John Hardy; Wesley C Warren; Evan E Eichler Journal: Nat Genet Date: 2008-09 Impact factor: 38.330