• IsoRankN

  • Referenced in 10 articles [sw08325]
  • describe IsoRankN (IsoRank-Nibble), a global multiple-network alignment tool based on spectral clustering ... algorithms for global network alignment in coverage and consistency on multiple alignments of the five...
  • Graemlin

  • Referenced in 5 articles [sw29736]
  • Graemlin: general and robust alignment of multiple large interaction networks. The recent proliferation of protein ... interaction networks has motivated research into network alignment: the cross-species comparison of conserved functional ... alignment algorithms to their limits. To find conserved functional modules in these new networks ... first algorithm capable of scalable multiple network alignment. Græmlin’s explicit model of functional evolution...
  • IsoRank

  • Referenced in 10 articles [sw08324]
  • algorithm for global alignment of multiple protein-protein inter- action (PPI) networks. The algorithm aims ... maximize the overall match across all input networks. This is, to our knowledge, the first ... field has focused on local network alignment. The intuition behind our algorithm is that...
  • SMETANA

  • Referenced in 1 article [sw34154]
  • efficient algorithm for alignment of multiple large-scale biological networks. In this scheme, we first ... measure between nodes that belong to different networks using a semi-Markov random walk model ... used to predict the alignment of multiple networks based on a greedy approach. We demonstrate ... outperforms many state-of-the-art network alignment techniques, in terms of computational efficiency, alignment...
  • Porter

  • Referenced in 4 articles [sw16910]
  • obtained from multiple sequence alignments, second stage filtering by recurrent neural networks, incorporation of long...
  • NetCoffee

  • Referenced in 1 article [sw34151]
  • accurate global alignment approach to identify functionally conserved proteins in multiple networks. Motivation: Owing ... Network alignments provide a systematic way to solve this problem. However, most existing alignment tools ... demand for faster and more efficient alignment tools is growing. Results: We present a fast ... find a global alignment of multiple protein–protein interaction networks. NetCoffee searches for a global...
  • NETAL

  • Referenced in 3 articles [sw34152]
  • find the best global network alignment. NETAL outperforms other global alignment methods in terms ... number of common Gene Ontology terms between aligned proteins. As the running time of NETAL ... NETAL can be easily expanded to multiple alignment algorithm. Furthermore, NETAL overpowers all other existing ... first server for global alignment of protein–protein interaction networks. Availability: Binaries supported on linux...
  • PCOAT

  • Referenced in 1 article [sw35662]
  • perform positional correlation analysis for protein multiple sequence alignment in order to identify structurally ... pairs, individual positions and networks of correlated positions, and utilize multiple sequence weighting and sampling ... relatively fast and is suitable for analyzing alignments containing large number of sequences. Availability...
  • VENLO

  • Referenced in 1 article [sw18647]
  • VENLO: Interactive Visual Exploration of Aligned Biological Networks and Their Evolution. To understand life ... evolution and function of biological networks in multiple species. Recently it has become possible ... resulting from these reconstructions consists of ancestral networks and gene trees. To analyze such data ... main visualization types: (a) as network alignments in 2.5D (or other known) layouts...
  • DeepContext

  • Referenced in 1 article [sw32556]
  • image depicting a 3D scene, our network aligns the observed scene with a predefined ... recognizes multiple objects in a single forward pass of a 3D convolutional neural network, capturing...
  • PSICOV

  • Referenced in 5 articles [sw17010]
  • made by identifying correlated mutations within multiple sequence alignments (MSAs), most commonly through the information ... performing normalized mutual information approach and Bayesian networks. For 118 out of 150 targets...
  • Bioclipse

  • Referenced in 5 articles [sw21445]
  • editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files ... graphical editor for sequences and alignments. CONCLUSION: Bioclipse 2 is equipped with advanced tools required ... takes full advantage of the Web and networked (Web/Cloud) services for more demanding calculations...
  • PrimAlign

  • Referenced in 1 article [sw34148]
  • propose a novel pairwise global network alignment algorithm, called PrimAlign, which is modeled ... with human, yeast and fruit fly PPI networks. The experimental results demonstrate that PrimAlign outperforms ... prevalent methods with statistically significant differences in multiple evaluation measures. PrimAlign, which is multi-platform ... networks and results suggest that popular topological measures do not reflect real precision of alignments...
  • HPAM

  • Referenced in 3 articles [sw10931]
  • complex promoter motifs that combines the neural network efficiency and ability of representing imprecise ... model by searching according to multiple criteria. We test our methodology by learning and predicting ... constitutes a special challenge due to the multiplicity of the RNA polymerase targets ... with other transcription factors, which sometimes require multiple functional binding sites even in close located...
  • StrBioLib

  • Referenced in 2 articles [sw16906]
  • biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence ... includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves...
  • eHive

  • Referenced in 2 articles [sw27408]
  • comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block ... three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments and (3) gene...
  • MetaPSICOV

  • Referenced in 1 article [sw17012]
  • global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor ... ability to accurately predict the long range network of hydrogen bonds, including correctly assigning...
  • vec_decomposition

  • Referenced in 1 article [sw22287]
  • pJ/word on the network). To increase memory locality at the hardware level and reduce energy ... instruction registers that are able to process multiple data with one arithmetic operator ... data structure that takes into account memory alignment constraints and avoids gather/scatter instructions that...
  • ANSYS

  • Referenced in 655 articles [sw00044]
  • ANSYS offers a comprehensive software suite that spans...
  • CGAL

  • Referenced in 355 articles [sw00118]
  • The goal of the CGAL Open Source Project...