[go: up one dir, main page]

Stormo, 2000 - Google Patents

Gene-finding approaches for eukaryotes

Stormo, 2000

View PDF @Free from Publisher
Document ID
4366030488820119389
Author
Stormo G
Publication year
Publication venue
Genome research

External Links

Snippet

The goal of this paper is to introduce the methods commonly used for predicting protein- coding regions in eukaryotic DNA, primarily for the benefit of those not familiar with the topic. This is not meant as a comprehensive review, nor do I describe in detail the underlying …
Continue reading at genome.cshlp.org (PDF) (other versions)

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
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/20—Handling natural language data
    • G06F17/21—Text processing
    • G06F17/22—Manipulating or registering by use of codes, e.g. in sequence of text characters
    • 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
    • G06F17/20—Handling natural language data
    • G06F17/21—Text processing
    • G06F17/24—Editing, e.g. insert/delete
    • 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
    • G06F17/30634—Querying
    • 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
    • G06F17/20—Handling natural language data
    • G06F17/27—Automatic analysis, e.g. parsing
    • 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
    • G06F19/18—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
    • 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
    • G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
    • G06F3/02—Input arrangements using manually operated switches, e.g. using keyboards or dials
    • G06F3/023—Arrangements for converting discrete items of information into a coded form, e.g. arrangements for interpreting keyboard generated codes as alphanumeric codes, operand codes or instruction codes
    • G06F3/0233—Character input methods
    • G06F3/0237—Character input methods using prediction or retrieval techniques
    • 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
    • G06Q—DATA 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
    • G06Q10/00—Administration; Management
    • G06Q10/10—Office automation, e.g. computer aided management of electronic mail or groupware; Time management, e.g. calendars, reminders, meetings or time accounting
    • 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
    • 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

Similar Documents

Publication Publication Date Title
Stormo Gene-finding approaches for eukaryotes
Salamov et al. Ab initio gene finding in Drosophila genomic DNA
Ohler et al. Identification and analysis of eukaryotic promoters: recent computational approaches
Zhang Computational prediction of eukaryotic protein-coding genes
Wu et al. GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Pavesi et al. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
Down et al. NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
Yao et al. CMfinder—a covariance model based RNA motif finding algorithm
Marioni et al. BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data
Bussemaker et al. Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis
Degroeve et al. SpliceMachine: predicting splice sites from high-dimensional local context representations
Rogic et al. Evaluation of gene-finding programs on mammalian sequences
DeCaprio et al. Conrad: gene prediction using conditional random fields
Burden et al. Improving promoter prediction Improving promoter prediction for the NNPP2. 2 algorithm: a case study using Escherichia coli DNA sequences
Weinberg et al. Sequence-based heuristics for faster annotation of non-coding RNA families
Sandve et al. Improved benchmarks for computational motif discovery
Malhis et al. Slider—maximum use of probability information for alignment of short sequence reads and SNP detection
Hajarnavis et al. A probabilistic model of 3′ end formation in Caenorhabditis elegans
Guyon et al. SA-Search: a web tool for protein structure mining based on a Structural Alphabet
Pereira et al. HattCI: fast and accurate attC site identification using hidden Markov models
Haeussler et al. Annotating genes and genomes with DNA sequences extracted from biomedical articles
Sarrazin-Gendron et al. Automated, customizable and efficient identification of 3D base pair modules with BayesPairing
Gutierrez et al. MembraneFold: Visualising transmembrane protein structure and topology
Solovyev et al. INFOGENE: a database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects
Pellegrini et al. TRStalker: an efficient heuristic for finding fuzzy tandem repeats