• Kenzo

  • Referenced in 65 articles [sw04861]
  • ideas of the second author about Effective Homology, mainly around the Serre and Eilenberg-Moore...
  • EAT

  • Referenced in 17 articles [sw09167]
  • symbolic software for effective homology computation. Kenzo: EAT (= Effective Algebraic Topology), the previous program. Before ... goal was the computation of the first homology groups of some loop spaces, for which ... designed to illustrate our methods of Effective Homology by a concrete experimental program...
  • CHomP

  • Referenced in 51 articles [sw09358]
  • nonlinear spaces and functions, within which homology is perhaps the most computable subset. In particular ... effort to develop and apply efficient and effective topologically based methods to the analysis...
  • SnapPea

  • Referenced in 163 articles [sw06873]
  • listed: volume, Chern-Simons invariant (if orientable), homology, symmetry or isometry group, shortest geodesic, chirality ... first step one has to find effective ways of eliminating a large number of gluings...
  • PHAT

  • Referenced in 41 articles [sw08780]
  • library for the computation of persistent homology. This task is usually split into two major ... suitable representation has an equally important effect on the practical performance as the choice...
  • BLAT

  • Referenced in 36 articles [sw16891]
  • query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions ... This paper describes how BLAT was optimized. Effects on speed and sensitivity are explored...
  • ChainCon

  • Referenced in 9 articles [sw12058]
  • ChainCon Software: Chain Contractions, Homology and Cohomology Software and Examples. The algorithms described ... programming language for optimal effectiveness and flexibility. Although a lot of effort was put into ... processing large data structures with reasonable effectiveness, it was primarily intended to serve ... small amount of code from the Computational Homology Project (CHomP) programming library, and thus...
  • 3DIGARS

  • Referenced in 1 article [sw36904]
  • structures and therefore is not effective for non-homologous sequence-based structure prediction. Thus ... optimization problem. To cope, we utilize an effective energy function (called 3DIGARS) and an advanced...
  • OreAlgebraicAnalysis

  • Referenced in 4 articles [sw15153]
  • Effective algebraic analysis approach to linear systems over Ore algebras. Physical systems are typically modeled ... algebraic viewpoint, using D-module theory and homological algebra techniques. The different types of systems...
  • PairProSVM

  • Referenced in 5 articles [sw35332]
  • proteins are important functional annotations. An effective and reliable subcellular localization method is necessary ... acid compositions even if most of the homologous sequences have been removed. PairProSVM was evaluated...
  • HSEpred

  • Referenced in 3 articles [sw25088]
  • values, based on a well-prepared non-homologous protein structure dataset. In particular, we employ ... five sequence-encoding schemes to examine their effects on the prediction performance. Our method could...
  • FastLSA

  • Referenced in 3 articles [sw01958]
  • Sequence alignment is a fundamental operation for homology search in bioinformatics ... trading space for operations. FastLSA can effectively adapt to use either linear or quadratic space...
  • MSACompro

  • Referenced in 1 article [sw38910]
  • PROMALS of using structural features and additional homologous sequences by slightly lower scores. Conclusion: MSACompro ... multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple...
  • CMfinder

  • Referenced in 6 articles [sw17265]
  • featuring novel integration of multiple techniques for effective search of motif space, and a Bayesian ... probabilistic model can be directly used for homology search, allowing iterative refinement of structural models...
  • PerlGP

  • Referenced in 3 articles [sw10501]
  • strongly typed tree-based GP with homologous crossover. User-defined grammars allow any valid Perl ... problems, particularly string-based ones. The effect of per-node, fixed and self-adapting crossover...
  • Socrates

  • Referenced in 1 article [sw34368]
  • idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours ... Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points...
  • BetaSCP

  • Referenced in 3 articles [sw08772]
  • important biomolecular applications such as a homology modeling, a docking simulation, a protein design ... optima within a reasonable computation time. The effectiveness and efficiency of the BetaSCP are experimentally...
  • DeepLoc

  • Referenced in 2 articles [sw42629]
  • annotated homologues exist, and for predicting the effects of sequence variants, it is desirable ... algorithms, including those relying on homology information...
  • SpeedHap

  • Referenced in 2 articles [sw35353]
  • reconstruction for (portions of) a pair of homologous human chromosomes from a single individual ... many gapped fragments and retains its effectiveness even when the input fragments have high rate...
  • MCScanX

  • Referenced in 1 article [sw29671]
  • subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes ... examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history...