Nothing Special   »   [go: up one dir, main page]

Regev, 2019 - Google Patents

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

Regev, 2019

View PDF
Document ID
12480257648990069726
Author
Regev A
Publication year

External Links

Snippet

Background: Accurate fusion transcript detection is essential for comprehensive characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been developed to predict fusions from RNA-seq, based on either read mapping or de …
Continue reading at dspace.mit.edu (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
    • G06F19/28Bioinformatics, 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
    • G06F19/18Bioinformatics, 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
    • G06F19/24Bioinformatics, 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
    • 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
    • G06F19/10Bioinformatics, 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
    • 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
    • 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
    • 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
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F21/00Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F8/00Arrangements for software engineering
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by the preceding groups
    • G01N33/48Investigating or analysing materials by specific methods not covered by the preceding groups biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing

Similar Documents

Publication Publication Date Title
Haas et al. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods
Heather et al. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities
Lee et al. Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score
Luebeck et al. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications
Yang et al. Analysis of whole transcriptome sequencing data: workflow and software
Kuchenbecker et al. IMSEQ—a fast and error aware approach to immunogenetic sequence analysis
Hsieh et al. Effect of de novo transcriptome assembly on transcript quantification
Fu et al. IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing
Chen et al. GeneFuse: detection and visualization of target gene fusions from DNA sequencing data
George et al. Effective function annotation through catalytic residue conservation
Yang et al. ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
Iacoangeli et al. DNAscan: personal computer compatible NGS analysis, annotation and visualisation
Mantini et al. Computational analysis of phosphoproteomics data in multi‐omics cancer studies
Simon et al. MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data
Chen et al. Deciphering oncogenic drivers: from single genes to integrated pathways
Santander et al. STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data
Karimi et al. Prospects and challenges of cancer systems medicine: from genes to disease networks
Tang et al. PASTA: splice junction identification from RNA-Sequencing data
Grigoriadis et al. CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction
Dehkordi et al. FaNDOM: Fast nested distance-based seeding of optical maps
Rajaby et al. SurVIndel: improving CNV calling from high-throughput sequencing data through statistical testing
Westphal et al. SMaSH: Sample matching using SNPs in humans
Koncz et al. Self-mediated positive selection of T cells sets an obstacle to the recognition of nonself
Petri et al. isONform: reference-free transcriptome reconstruction from Oxford Nanopore data
Namiki et al. Acceleration of sequence clustering using longest common subsequence filtering