Corvelo et al., 2018 - Google Patents
taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable timeCorvelo et al., 2018
View PDF- Document ID
- 3844783381534623466
- Author
- Corvelo A
- Clarke W
- Robine N
- Zody M
- Publication year
- Publication venue
- Genome research
External Links
Snippet
High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a …
- 229920000160 (ribonucleotides)n+m 0 abstract description 5
Classifications
-
- 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
- G06F19/28—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
- G06F19/24—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
- 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
- G06F19/16—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for molecular structure, e.g. structure alignment, structural or functional relations, protein folding, domain topologies, drug targeting using structure data, involving two-dimensional or three-dimensional structures
-
- 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
- G06F17/30312—Storage and indexing structures; Management thereof
- G06F17/30321—Indexing structures
-
- 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
- G06F19/14—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
- G06F9/00—Arrangements for programme control, e.g. control unit
- G06F9/06—Arrangements for programme control, e.g. control unit using stored programme, i.e. using internal store of processing equipment to receive and retain programme
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F7/00—Methods or arrangements for processing data by operating upon the order or content of the data handled
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
Similar Documents
Publication | Publication Date | Title |
---|---|---|
Corvelo et al. | taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time | |
Ondov et al. | Mash Screen: high-throughput sequence containment estimation for genome discovery | |
Ekim et al. | Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer | |
Kim et al. | Centrifuge: rapid and sensitive classification of metagenomic sequences | |
Dilthey et al. | Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps | |
Menzel et al. | Fast and sensitive taxonomic classification for metagenomics with Kaiju | |
Mu et al. | Fast and accurate read alignment for resequencing | |
Rosen et al. | Metagenome Fragment Classification Using N‐Mer Frequency Profiles | |
Zou et al. | Supersecondary structure prediction using Chou's pseudo amino acid composition | |
Al-Ghalith et al. | NINJA-OPS: fast accurate marker gene alignment using concatenated ribosomes | |
Zhang et al. | PEAR: a fast and accurate Illumina Paired-End reAd mergeR | |
Clark et al. | Evolutionary rate covariation reveals shared functionality and coexpression of genes | |
Sirén et al. | Rapid discovery of novel prophages using biological feature engineering and machine learning | |
Alser et al. | From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures | |
Müller et al. | MetaCache: context-aware classification of metagenomic reads using minhashing | |
Liu et al. | A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures | |
Zhang et al. | RNA-Skim: a rapid method for RNA-Seq quantification at transcript level | |
Borozan et al. | Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification | |
Luo et al. | Metagenomic binning through low-density hashing | |
Shah et al. | TIPP2: metagenomic taxonomic profiling using phylogenetic markers | |
Al-Ghalith et al. | BURST enables mathematically optimal short-read alignment for big data | |
Mount | Using BLOSUM in sequence alignments | |
Menzel et al. | Kaiju: Fast and sensitive taxonomic classification for metagenomics | |
Wang et al. | Improving contig binning of metagenomic data using d 2 S d _2^ S oligonucleotide frequency dissimilarity | |
Homer et al. | Local alignment of two-base encoded DNA sequence |