[go: up one dir, main page]
More Web Proxy on the site http://driver.im/

Liu et al., 2014 - Google Patents

CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding

Liu et al., 2014

View HTML
Document ID
2041873819173475081
Author
Liu Y
Popp B
Schmidt B
Publication year
Publication venue
PloS one

External Links

Snippet

The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome …
Continue reading at journals.plos.org (HTML) (other versions)

Classifications

    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/22Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/18Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30289Database design, administration or maintenance
    • G06F17/30303Improving data quality; Data cleansing
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/28Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/30Medical informatics, i.e. computer-based analysis or dissemination of patient or disease data
    • G06F19/34Computer-assisted medical diagnosis or treatment, e.g. computerised prescription or delivery of medication or diets, computerised local control of medical devices, medical expert systems or telemedicine
    • G06F19/345Medical expert systems, neural networks or other automated diagnosis
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/14Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/24Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/16Bioinformatics, 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/50Computer-aided design
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F9/00Arrangements for programme control, e.g. control unit
    • G06F9/06Arrangements for programme control, e.g. control unit using stored programme, i.e. using internal store of processing equipment to receive and retain programme
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F7/00Methods or arrangements for processing data by operating upon the order or content of the data handled
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F11/00Error detection; Error correction; Monitoring
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06QDATA PROCESSING SYSTEMS OR METHODS, SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES, NOT OTHERWISE PROVIDED FOR
    • G06Q50/00Systems or methods specially adapted for a specific business sector, e.g. utilities or tourism
    • G06Q50/10Services
    • G06Q50/22Health care, e.g. hospitals; Social work
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F8/00Arrangements for software engineering
    • G06F8/40Transformations of program code
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06NCOMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N99/00Subject matter not provided for in other groups of this subclass
    • G06N99/005Learning machines, i.e. computer in which a programme is changed according to experience gained by the machine itself during a complete run

Similar Documents

Publication Publication Date Title
Liu et al. CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding
Rakocevic et al. Fast and accurate genomic analyses using genome graphs
Dilthey et al. Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Tini et al. Multi-omics integration—a comparison of unsupervised clustering methodologies
van Kempen et al. Foldseek: fast and accurate protein structure search
Luo et al. SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner
Hatem et al. Benchmarking short sequence mapping tools
Liu et al. CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform
Li et al. Fast and accurate long-read alignment with Burrows–Wheeler transform
Ebersberger et al. HaMStR: profile hidden markov model based search for orthologs in ESTs
Wright et al. From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools
Blom et al. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
Alser et al. From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
Torri et al. Next generation sequence analysis and computational genomics using graphical pipeline workflows
Lee et al. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Mirarab et al. FastSP: linear time calculation of alignment accuracy
Singh et al. SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model
Firtina et al. BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
Sirén et al. Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit
Prezza et al. SNPs detection by eBWT positional clustering
Ochoa et al. Beyond the E-value: stratified statistics for protein domain prediction
Loka et al. Reliable variant calling during runtime of Illumina sequencing
Wilton et al. Performance optimization in DNA short-read alignment
Ramachandran et al. HELLO: improved neural network architectures and methodologies for small variant calling
Manfredi et al. ISPRED-SEQ: Deep neural networks and embeddings for predicting interaction sites in protein sequences