
Kenzo
 Referenced in 65 articles
[sw04861]
 ideas of the second author about Effective Homology, mainly around the Serre and EilenbergMoore...

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, ChernSimons 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 nonhomologous sequencebased 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 Dmodule 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 wellprepared nonhomologous protein structure dataset. In particular, we employ ... five sequenceencoding 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 treebased GP with homologous crossover. Userdefined grammars allow any valid Perl ... problems, particularly stringbased ones. The effect of pernode, fixed and selfadapting crossover...

Socrates
 Referenced in 1 article
[sw34368]
 idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours ... Socrates has singlenucleotide resolution, identifies microhomologies 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...