[go: up one dir, main page]

Batzoglou, 2005 - Google Patents

The many faces of sequence alignment

Batzoglou, 2005

View PDF
Document ID
11911094982320668738
Author
Batzoglou S
Publication year
Publication venue
Briefings in bioinformatics

External Links

Snippet

Starting with the sequencing of the mouse genome in 2002, we have entered a period where the main focus of genomics will be to compare multiple genomes in order to learn about human biology and evolution at the DNA level. Alignment methods are the main …
Continue reading at academic.oup.com (PDF) (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
    • G06F19/24Bioinformatics, 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
    • G06F19/18Bioinformatics, 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
    • 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
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/20Bioinformatics, 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
    • 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
    • G06F17/30Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/3061Information retrieval; Database structures therefor; File system structures therefor of unstructured textual data
    • G06F17/30634Querying
    • G06F17/30657Query processing
    • G06F17/30675Query execution
    • 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
    • G06F17/00Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/3061Information retrieval; Database structures therefor; File system structures therefor of unstructured textual data
    • G06F17/30613Indexing
    • G06F17/30619Indexing indexing structures
    • 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
    • G06F17/30312Storage and indexing structures; Management thereof
    • G06F17/30321Indexing structures
    • 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
    • G06F19/12Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for modelling or simulation in systems biology, e.g. probabilistic or dynamic models, gene-regulatory networks, protein interaction networks or metabolic networks
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/70Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
    • G06F19/708Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for data visualisation, e.g. molecular structure representations, graphics generation, display of maps or networks or other visual representations
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/70Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
    • G06F19/702Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for analysis and planning of chemical reactions and syntheses, e.g. synthesis design, reaction prediction, mechanism elucidation
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10Complex mathematical operations
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F3/00Input 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
    • 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

Similar Documents

Publication Publication Date Title
Batzoglou The many faces of sequence alignment
Williams et al. Indexing and retrieval for genomic databases
Giancarlo et al. Textual data compression in computational biology: a synopsis
Eddy Profile hidden Markov models.
Barrett et al. Scoring hidden Markov models
US10346551B2 (en) Systems, methods and computer-accessible mediums for utilizing pattern matching in stringomes
Orengo et al. Bioinformatics: genes, proteins and computers
Brejová et al. Finding patterns in biological sequences
Ndiaye et al. When less is more: sketching with minimizers in genomics
Comin et al. Beyond fixed-resolution alignment-free measures for mammalian enhancers sequence comparison
Vaddadi et al. Read mapping on genome variation graphs
Abouelhoda et al. String mining in bioinformatics
Qian et al. Performance of an iterated T-HMM for homology detection
Carlson et al. BEAM: a beam search algorithm for the identification of cis-regulatory elements in groups of genes
Wong et al. Predicting approximate protein-dna binding cores using association rule mining
Narasimhan et al. Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection
Li et al. Seeding with minimized subsequence
Roddy et al. nail: software for high-speed, high-sensitivity protein sequence annotation
Dewey Whole-genome alignments and polytopes for comparative genomics
Brejová et al. Pattern discovery: Methods and software
JP2003256433A (en) Gene structure analysis method and apparatus
Horton et al. RaPiDS: an algorithm for rapid expression profile database search
Chan et al. TFBS identification by position-and consensus-led genetic algorithm with local filtering
Pavesi et al. Methods for pattern discovery in unaligned biological sequences
Rajasekaran Computational techniques for motif search