• ViennaRNA

  • Referenced in 23 articles [sw10504]
  • probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which ... generates all suboptimal structures within a given energy range of the optimal energy. For secondary...
  • OpenACC

  • Referenced in 29 articles [sw11090]
  • efficient than low-level APIs, even if suboptimal performance is achieved...
  • AdaBoost.RT

  • Referenced in 14 articles [sw08520]
  • AdaBoost procedure. Thus, it requires selecting the suboptimal value of the error threshold to demarcate...
  • SPRINT

  • Referenced in 11 articles [sw01362]
  • design space often leads to a suboptimal implementation. To support our systematic C-based design...
  • DSP

  • Referenced in 11 articles [sw05421]
  • even if the master problem is solved suboptimally. DSP can solve instances specified...
  • RNAsubopt

  • Referenced in 6 articles [sw10506]
  • RNAsubopt 2.1.8: calculate suboptimal secondary structures of RNAs. reads RNA sequences from stdin ... default −e mode) calculates all suboptimal secondary structures within a user defined energy range above ... minimum free energy (mfe). It prints the suboptimal structures in dot−bracket notation followed...
  • DIAL

  • Referenced in 6 articles [sw13837]
  • semiglobal (modified to yield motif search). Suboptimal alignments are optionally returned, and also Boltzmann pair ... optimal alignment. If a non-zero suboptimal alignment score ratio is entered, then the semiglobal ... superposition for the optimal (and suboptimal) alignment of query to target. Although graphical output...
  • RNAshapes

  • Referenced in 7 articles [sw07960]
  • added a number of useful features like suboptimal folding with correct dangling energies, structure graph...
  • DIALIGN-TX

  • Referenced in 7 articles [sw12751]
  • random similarities and can therefore lead to suboptimal results. In this paper, we present DIALIGN...
  • casper

  • Referenced in 5 articles [sw09370]
  • based on such summaries and are hence suboptimal. Further, they have limited flexibility in accounting...
  • FACTORIZE

  • Referenced in 5 articles [sw10039]
  • method on their own can lead to suboptimal choices; even MATLAB experts can make...
  • na8

  • Referenced in 5 articles [sw11513]
  • much simpler than most optimal or seven suboptimal reduction techniques presently available, since it requires...
  • BioNet

  • Referenced in 5 articles [sw13828]
  • scoring of nodes, methods for optimal, suboptimal and fast heuristic searches, as well as routines...
  • Classbox/J

  • Referenced in 5 articles [sw30250]
  • introduce anomalies such as duplicated code, suboptimal inheritance relationships and a proliferation of run-time...
  • Charmy

  • Referenced in 4 articles [sw11046]
  • move forward to the construction of a suboptimal software architecture. Charmy aims to provide...
  • WONDER

  • Referenced in 4 articles [sw35432]
  • ridge. Thus, all averaging methods are suboptimal. We also propose a new Weighted ONe-shot...
  • RNAspa

  • Referenced in 2 articles [sw17131]
  • that in a list of several hundred suboptimal minimal free energy (MFE) predictions, as provided ... similar to the true, correct one. The suboptimal solutions of each molecule are represented ... allows us to more deeply explore the suboptimal structure space. Conclusion: The algorithm was tested...
  • Graph Matching Toolkit

  • Referenced in 2 articles [sw09487]
  • paper introduced several powerful approximations for fast suboptimal graph edit distance computation. The contribution ... self standing software tool integrating these suboptimal graph matching algorithms. It is about being made...
  • RNAmute

  • Referenced in 2 articles [sw17059]
  • point mutations efficiently by initially calculating all suboptimal solutions, after which only the mutations that ... stabilize the suboptimal solutions and destabilize the optimal one are considered as candidates for being...
  • UNDX

  • Referenced in 3 articles [sw03438]
  • proposed method can find empirically optimal and suboptimal lenses. We also apply the proposed method...