Kotamarti et al., 2009 - Google Patents
Targeted genomic signature profiling with quasi-alignment statisticsKotamarti et al., 2009
View PDF- Document ID
- 10916604813076359153
- Author
- Kotamarti R
- Raiford D
- Hahsler M
- Wang Y
- McGee M
- Dunham M
- Publication year
External Links
Snippet
Genome databases continue to expand with no change in the basic format of sequence data. The prevalent use of the Classic alignment based search tools like BLAST have significantly pushed the limits of Genome Isolate research. The relatively new frontier of …
- 239000011159 matrix material 0 abstract description 79
Classifications
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
- G06F17/30386—Retrieval requests
- G06F17/30424—Query processing
- G06F17/30533—Other types of queries
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/22—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/24—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
- G06F17/30289—Database design, administration or maintenance
- G06F17/30303—Improving data quality; Data cleansing
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/20—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/28—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/18—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/14—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for phylogeny or evolution, e.g. evolutionarily conserved regions determination or phylogenetic tree construction
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/3061—Information retrieval; Database structures therefor; File system structures therefor of unstructured textual data
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
- G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
- G06K9/62—Methods or arrangements for recognition using electronic means
- G06K9/6217—Design or setup of recognition systems and techniques; Extraction of features in feature space; Clustering techniques; Blind source separation
- G06K9/6228—Selecting the most significant subset of features
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N99/00—Subject matter not provided for in other groups of this subclass
- G06N99/005—Learning machines, i.e. computer in which a programme is changed according to experience gained by the machine itself during a complete run
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
- G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
- G06K9/62—Methods or arrangements for recognition using electronic means
- G06K9/6267—Classification techniques
- G06K9/6279—Classification techniques relating to the number of classes
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computer systems based on biological models
- G06N3/12—Computer systems based on biological models using genetic models
- G06N3/126—Genetic algorithms, i.e. information processing using digital simulations of the genetic system
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N7/00—Computer systems based on specific mathematical models
- G06N7/005—Probabilistic networks
Similar Documents
Publication | Publication Date | Title |
---|---|---|
Menzel et al. | Fast and sensitive taxonomic classification for metagenomics with Kaiju | |
Mock et al. | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks | |
US20230238081A1 (en) | Artificial intelligence analysis of rna transcriptome for drug discovery | |
Cilibrasi et al. | A fast quartet tree heuristic for hierarchical clustering | |
Regueira‐Iglesias et al. | Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis | |
Tillquist et al. | Low-dimensional representation of genomic sequences | |
Zimek et al. | A study of hierarchical and flat classification of proteins | |
Dutta et al. | Parameterized syncmer schemes improve long-read mapping | |
CN113555062A (en) | Data analysis system and analysis method for genome base variation detection | |
JP2008533619A (en) | System, method and computer program for non-binary sequence comparison | |
Brinda | Novel computational techniques for mapping and classification of Next-Generation Sequencing data | |
Kouchaki et al. | A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns | |
Kim et al. | Metabuli: sensitive and specific metagenomic classification via joint analysis of amino acid and DNA | |
Jaffe et al. | Spectral neighbor joining for reconstruction of latent tree models | |
Kotamarti et al. | Targeted genomic signature profiling with quasi-alignment statistics | |
Vallat et al. | A template‐finding algorithm and a comprehensive benchmark for homology modeling of proteins | |
Dehmer et al. | Entropy bounds for hierarchical molecular networks | |
Das et al. | Sketching and sampling approaches for fast and accurate long read classification | |
Ulrich et al. | Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters | |
Kotamarti et al. | Analyzing taxonomic classification using extensible Markov models | |
De Sanctis et al. | A theoretical analysis of taxonomic binning accuracy | |
Gerniers et al. | MicroCellClust 2: a hybrid approach for multivariate rare cell mining in large-scale single-cell data | |
Hassan et al. | Integrated rules classifier for predicting pathogenic non-synonymous single nucleotide variants in human | |
US20200357484A1 (en) | Method for simultaneous multivariate feature selection, feature generation, and sample clustering | |
Bennett et al. | SeqWho: Reliable, rapid determination of sequence file identity using k-mer frequencies |