Compressed q-Gram Indexing for Highly Repetitive Biological Sequences

No abstract is available for this paper.

• Publication year

  2010

• Venue

  International Conferences on Biological Information and Biomedical Engineering

• Publication date

  2010-05-31

• Fields of study

  Biology, Computer Science

• Identifiers
  DOI 10.1109/BIBE.2010.22
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Human Behaviour and the Principle of Least Effort: an Introduction to Human Ecology

  2012cited by this paper
• Storage and Retrieval of Individual Genomes

  2009influential reference
• Self-indexed Text Compression Using Straight-Line Programs

  2009influential reference
• Practical Rank/Select Queries over Arbitrary Sequences

  2008cited by this paper
• A Simple Statistical Algorithm for Biological Sequence Compression

  2007cited by this paper
• Compressed Text Indexes with Fast Locate

  2007cited by this paper
• Compressed full-text indexes

  2007cited by this paper
• Breakthrough of the year. Human genetic variation.

  2007cited by this paper
• Advanced sequencing technologies and their wider impact in microbiology

  2007cited by this paper
• Inverted Files Versus Suffix Arrays for Locating Patterns in Primary Memory

  2006influential reference
• Genomes for all.

  2006cited by this paper
• A simple and fast DNA compressor

  2004cited by this paper
• A fully linear-time approximation algorithm for grammar-based compression

  2003cited by this paper
• Succinct Representations of Permutations

  2003cited by this paper
• Flexible Pattern Matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences

  2002cited by this paper
• DNA Data Compression in the Post Genome Era

  2001cited by this paper
• A compression algorithm for DNA sequences and its applications in genome comparison

  2000cited by this paper
• Offline dictionary-based compression

  2000cited by this paper
• Compressing Integers for Fast File Access

  1999cited by this paper
• Protein is incompressible

  1999cited by this paper
• A guaranteed compression scheme for repetitive DNA sequences

  1996cited by this paper
• A New Challenge for Compression Algorithms: Genetic Sequences

  1994cited by this paper
• Practical fast searching in strings

  1980cited by this paper
• A universal algorithm for sequential data compression

  1977cited by this paper

• INTS1 is required for maintaining accurate transcriptional integrity and behavior in zebrafish

  2025cites this paper
• Efficient Grammar Compression via RLZ-based RePair

  2025cites this paper
• Re2Pair: Increasing the Scalability of RePair by Decreasing Memory Usage

  2024cites this paper
• Memory-Efficient Assembly Using Flye

  2021cites this paper
• Grammar-Compressed Indexes with Logarithmic Search Time

  2020cites this paper
• Design and Development of Bioinformatics Feature Based DNA Sequence Data Compression Algorithm

  2020cites this paper
• On the Reproducibility of Experiments of Indexing Repetitive Document Collections

  2019cites this paper
• Efficient Storage of Genomic Sequences in High Performance Computing Systems

  2019cites this paper
• Optimized Context Weighting for the Compression of the Un-repetitive Genome Sequence Fragment

  2018cites this paper
• On the Reproducibility of Experiments of Indexing Repetitive Document

  2018cites this paper
• Cross-Browser Differences Detection Based on an Empirical Metric for Web Page Visual Similarity

  2018cites this paper
• FROG: Inference from knowledge base for missing value imputation

  2018cites this paper
• Pan-Genome Storage and Analysis Techniques.

  2018cites this paper
• Practical and Effective Re-Pair Compression

  2017cites this paper
• Visual Similarity Analysis of Web Pages based on Gestalt Theory

  2017cites this paper
• Practical compressed string dictionaries

  2016cites this paper
• Universal indexes for highly repetitive document collections

  2016influential citation
• Document retrieval on repetitive string collections

  2016cites this paper
• Nucleotide Sequence Similarity Search Using Techniques from Content-Based Image Retrieval

  2015cites this paper
• Advances in stringology and applications : from combinatorics via genomic analysis to computational linguistics

  2015cites this paper
• Semi-dynamic Compact Index for Short Patterns and Succinct van Emde Boas Tree

  2015cites this paper
• Locally Compressed Suffix Arrays

  2015cites this paper
• Correction: Indexes of Large Genome Collections on a PC

  2015cites this paper
• Compressing Similar Biological Sequences Using FM-Index

  2014cites this paper
• Indexes of Large Genome Collections on a PC

  2014cites this paper
• Practical Compressed Suffix Trees

  2013cites this paper
• Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data

  2013cites this paper
• Genome compression: a novel approach for large collections

  2013cites this paper
• Document Listing on Versioned Documents

  2013cites this paper
• Efficient direct search on compressed genomic data

  2013cites this paper
• DACs: Bringing direct access to variable-length codes

  2013cites this paper
• On compressing and indexing repetitive sequences

  2013cites this paper
• A deoxyribonucleic acid Compression Algorithm using Auto-Regression and Swarm Intelligence

  2013cites this paper
• Space-Efficient Data Structures for Information Retrieval

  2013influential citation
• Aide à l'analyse de traces d'exécution dans le contexte des microcontrôleurs 32 bits. (Assit to execution trace analysis in the microcontrollers 32 bits context)

  2013cites this paper
• Efficient processing of substring match queries with inverted variable-length gram indexes

  2013cites this paper
• ESTRUCTURAS DE DATOS SUCINTAS PARA RECUPERACIÓN DE DOCUMENTOS

  2013cites this paper
• Compressed Suffix Trees for Repetitive Texts

  2012cites this paper
• Compressed Full-Text Indexes for Highly Repetitive Collections

  2012cites this paper
• Querying Highly Similar Structured Sequences via Binary Encoding and Word Level Operations

  2012cites this paper
• Indexing Highly Repetitive Collections

  2012cites this paper
• Iterative Dictionary Construction for Compression of Large DNA Data Sets

  2012cites this paper
• Combinatorial Algorithms

  2012cites this paper
• Wavelet trees: A survey

  2012cites this paper
• Lightweighting the Web of Data through Compact RDF/HDT

  2011cites this paper
• Self-Indexed Grammar-Based Compression

  2011cites this paper
• Robust relative compression of genomes with random access

  2011cites this paper
• Searching for Compact Hierarchical Structures in DNA by means of the Smallest Grammar Problem

  2011cites this paper
• Self-indexing Based on LZ77

  2011cites this paper
• Engineering Relative Compression of Genomes

  2011cites this paper
• Improved Grammar-Based Compressed Indexes

  2011cites this paper
• Self-Index Based on LZ77

  2011cites this paper
• Space Efficient Wavelet Tree Construction

  2011cites this paper
• Self-Index based on LZ77 (thesis)

  2011cites this paper
• Algorithms and Compressed Data Structures for Information Retrieval

  2011cites this paper
• Indexes for highly repetitive document collections

  2011cites this paper
• An Online Algorithm for Lightweight Grammar-Based Compression

  2011cites this paper
• TESIS PARA OPTAR AL GRADO DE MAG ISTER EN CIENCIAS, MENCI ON COMPUTACI ON

  2010cites this paper
• Practical Compressed Suffix Trees

  2010cites this paper