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DECIPHER is a software that can be used to decipher and manage biological sequences efficiently using the programming language R. Features ...
The bulge corremoval algorithm can be summarized as follows: a simple bulge is formed by two small and similar paths (P and Q) connecting the same hubs. If P is a non-branching path (h-path), then SPAdes maps every edge in P to an edge projection in Q and removes P from the graph, as a result the coverage of Q increases.
The source code is licensed under Apache License and available on GitHub. [6] InfoWorld magazine awarded the library "The best machine learning tools" in 2017. [11] along with TensorFlow, Pytorch, XGBoost and 8 other libraries. Kaggle listed CatBoost as one of the most frequently used machine learning (ML) frameworks in the world.
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
server and repository for protein structure models Protein model databases AAindex: database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials Protein model databases BioGRID: Samuel Lunenfeld Research Institute: general repository for interaction datasets Protein-protein and other molecular interactions
The LightGBM algorithm utilizes two novel techniques called Gradient-Based One-Side Sampling (GOSS) and Exclusive Feature Bundling (EFB) which allow the algorithm to run faster while maintaining a high level of accuracy. [13] LightGBM works on Linux, Windows, and macOS and supports C++, Python, [14] R, and C#. [15]
PCAHIER, [17] another binning algorithm developed by the Georgia Institute of Technology., employs n-mer oligonucleotide frequencies as the features and adopts a hierarchical classifier (PCAHIER) for binning short metagenomic fragments. The principal component analysis was used to reduce the high dimensionality of the feature space.
DECIPHER is a web-based resource and database of genomic variation data from analysis of patient DNA. [ 1 ] [ 2 ] [ 3 ] It documents submicroscopic chromosome abnormalities ( microdeletions and duplications ) and pathogenic sequence variants (single nucleotide variants - SNVs, Insertions, Deletions, InDels), from over 25000 patients and maps ...