• GQTPAR

  • Referenced in 325 articles [sw07451]
  • quadratic function subject to an ellipsoidal constraint and show that this algorithm is guaranteed ... prove that under reasonable assumptions the sequence generated by Newton’s method has a limit...
  • CONLIN

  • Referenced in 47 articles [sw14151]
  • constraints. The primary optimization problem is therefore replaced with a sequence of explicit approximate problems ... replaced with a sequence of approximate quadratic subproblems with non-negativity constraints on the dual...
  • SHOT

  • Referenced in 20 articles [sw15630]
  • defined by linear and nonlinear constraints. A sequence of linear or quadratic integer-relaxed subproblems...
  • SLIDE

  • Referenced in 8 articles [sw08449]
  • ensures a given constraint holds a number of times down a sequence of variables ... special case of CardPath where the slid constraint must hold always, can be used ... encode a wide range of sliding sequence constraints including CardPath itself. We consider...
  • CAP3

  • Referenced in 17 articles [sw08935]
  • generation of consensus sequences. The program also uses forward–reverse constraints to correct assembly errors ... CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct ... pass data with forward–reverse constraints...
  • QSDPNAL

  • Referenced in 33 articles [sw18799]
  • linear systems of equations under certain subspace constraints. More specifically, simpler and yet better conditioned ... sequences are constructed to alleviate the numerical difficulties brought about by the crucial subspace constraints...
  • FEASPUMP

  • Referenced in 133 articles [sw04802]
  • clever way to round a sequence of fractional solutions of the LP relaxation, until ... diving-like procedure based on rounding and constraint propagation-a basic tool in Constraint Programming...
  • SOPRA

  • Referenced in 8 articles [sw12607]
  • reads via statistical optimization. Background: High throughput sequencing (HTS) platforms produce gigabases of short read ... large subset of simultaneously satisfiable mate pair constraints to achieve a balance between the size ... been invoked in the context of shotgun sequencing and scaffold building for previous generation ... core set of consistent constraints. For SOLiD sequencer data, SOPRA uses a dynamic programming approach...
  • SDPEN

  • Referenced in 21 articles [sw05152]
  • objective function and of the constraints can be neither calculated nor explicitly approximated. Hence, every ... sequence of approximate minimizations of a merit function where penalization of constraint violation is progressively...
  • PROMALS3D

  • Referenced in 3 articles [sw16918]
  • homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments ... dimensional structures, and combines them with sequence-based constraints of profile–profile alignments ... based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment...
  • MuSiC

  • Referenced in 3 articles [sw35658]
  • MuSiC: a tool for multiple sequence alignment with constraints. MuSiC is a web server ... constrained alignment of a set of sequences, such that the user-specified residues/nucleotides are aligned ... protein/DNA/RNA sequences and a set of user-specified constraints, each with a fragment of residue/nucleotide ... input sequences whose residues/nucleotides exhibit a given degree of similarity to a constraint are aligned...
  • TRICE

  • Referenced in 46 articles [sw05197]
  • strict feasibility with respect to the bound constraints by using an affine scaling method proposed ... model and on the trial steps, the sequence of iterates generated by the algorithms ... special cases, current results for only equality constraints and for only simple bounds.par Numerical results...
  • MatrixPlot

  • Referenced in 1 article [sw35918]
  • MatrixPlot: visualizing sequence constraints. MatrixPlot is a program for making high-quality matrix plots, such ... mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional...
  • WPM3

  • Referenced in 6 articles [sw41870]
  • into a sequence of SAT decision problems where Pseudo-Boolean (PB) constraints may be introduced ... order to identify the most suitable PB constraints, some algorithms (core-guided) analyze the unsatisfiable ... from the previous SAT problems in the sequence while refining the lower bound. In this ... used to encode more efficient PB constraints and enables the algorithm to obtain assignments...
  • CLPS-B

  • Referenced in 7 articles [sw00132]
  • Constraint Logic Programming with sets. This approach is used to animate and generate test sequences ... CLPS-B, is described in terms of constraint domains, consistency verification and constraint propagation...
  • COBALT

  • Referenced in 1 article [sw38912]
  • COBALT: constraint-based alignment tool for multiple protein sequences. Motivation: A tool that simultaneously aligns ... multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between ... constraint based alignment tool that implements a general framework for multiple alignment of protein sequences ... collection of pairwise constraints derived from database searches, sequence similarity and user input, combines these...
  • DFL

  • Referenced in 32 articles [sw05163]
  • several variables subject to simple bound constraints where some of the variables are restricted ... satisfied by the limit points of the sequences they produce...
  • DARN!

  • Referenced in 4 articles [sw00186]
  • some input genomic sequence(s).Darn uses a weighted constraint solver to localize the portions...
  • OBSTRUCT

  • Referenced in 3 articles [sw16886]
  • sequence set according to structural resolution and sequence similarity. A program OBSTRUCT has been developed ... subset according to specific constraints from a set of protein sequences whose tertiary structures have...
  • cosmoGUI

  • Referenced in 1 article [sw36152]
  • cosmoGUI allows the user to interactively define constraint sets that can be used ... motifs in a set of DNA sequences. The constraints can be either adapted from...