Introduction to algorithms
Approximate string-matching with q-grams and maximal matches
Theoretical Computer Science - Selected papers of the Combinatorial Pattern Matching School
Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
Efficient implementation of suffix trees
Software—Practice & Experience
Genetic sequence data retrieval and manipulation based on generalized suffix trees
Genetic sequence data retrieval and manipulation based on generalized suffix trees
An orthogonally persistent Java
ACM SIGMOD Record
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
q-gram based database searching using a suffix array (QUASAR)
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
The string B-tree: a new data structure for string search in external memory and its applications
Journal of the ACM (JACM)
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
Managing gigabytes (2nd ed.): compressing and indexing documents and images
Managing gigabytes (2nd ed.): compressing and indexing documents and images
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
On effective multi-dimensional indexing for strings
SIGMOD '00 Proceedings of the 2000 ACM SIGMOD international conference on Management of data
Reducing the space requirement of suffix trees
Software—Practice & Experience
A guided tour to approximate string matching
ACM Computing Surveys (CSUR)
Journal of Algorithms
An efficient object promotion algorithm for persistent object systems
Software—Practice & Experience
Fully Integrated Data Environments: Persistent Programming Languages, Object Stores, and Programmingenvironments
Providing Orthogonal Persistence for Java (Extended Abstract)
ECCOP '98 Proceedings of the 12th European Conference on Object-Oriented Programming
Evolutionary Data Conversion in the PJama Persistent Language
Proceedings of the Workshop on Object-Oriented Technology
Approximate String-Matching over Suffix Trees
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Architecture of the PEVM: A High-Performance Orthogonally Persistent Java Virtual Machine
POS-9 Revised Papers from the 9th International Workshop on Persistent Object Systems
Overcoming the Memory Bottleneck in Suffix Tree Construction
FOCS '98 Proceedings of the 39th Annual Symposium on Foundations of Computer Science
A Review of the Rationale and Architectures of PJama: a Durable, Flexible, Evolvable and Scalable Orthogonally Persistent Programming Platform
Orthogonal Persistence for the Java[tm] Platform: Specification and Rationale
Orthogonal Persistence for the Java[tm] Platform: Specification and Rationale
Database Allocation Strategies for Parallel BLAST Evaluation on Clusters
Distributed and Parallel Databases
A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays
COCOON '02 Proceedings of the 8th Annual International Conference on Computing and Combinatorics
DEXA '01 Proceedings of the 12th International Conference on Database and Expert Systems Applications
The building of BODHI, a bio-diversity database system
Information Systems - Special issue: Data management in bioinformatics
Accelerating Approximate Subsequence Search on Large Protein Sequence Databases
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
A parallel algorithm for the extraction of structured motifs
Proceedings of the 2004 ACM symposium on Applied computing
SPINE: Putting Backbone into String Indexing
ICDE '04 Proceedings of the 20th International Conference on Data Engineering
Engineering a Fast Online Persistent Suffix Tree Construction
ICDE '04 Proceedings of the 20th International Conference on Data Engineering
Distance-function design and fusion for sequence data
Proceedings of the thirteenth ACM international conference on Information and knowledge management
Constructing Suffix Tree for Gigabyte Sequences with Megabyte Memory
IEEE Transactions on Knowledge and Data Engineering
Practical methods for constructing suffix trees
The VLDB Journal — The International Journal on Very Large Data Bases
Exact match search in sequence data using suffix trees
Proceedings of the 14th ACM international conference on Information and knowledge management
Reference-based indexing of sequence databases
VLDB '06 Proceedings of the 32nd international conference on Very large data bases
Constructing large suffix trees on a computational grid
Journal of Parallel and Distributed Computing
Survey on index based homology search algorithms
The Journal of Supercomputing
Genome-scale disk-based suffix tree indexing
Proceedings of the 2007 ACM SIGMOD international conference on Management of data
Searching on the secondary structure of protein sequences
VLDB '02 Proceedings of the 28th international conference on Very Large Data Bases
Indexing schemes for similarity search in datasets of short protein fragments
Information Systems
OASIS: an online and accurate technique for local-alignment searches on biological sequences
VLDB '03 Proceedings of the 29th international conference on Very large data bases - Volume 29
Practical suffix tree construction
VLDB '04 Proceedings of the Thirtieth international conference on Very large data bases - Volume 30
PSIST: A scalable approach to indexing protein structures using suffix trees
Journal of Parallel and Distributed Computing
The SBC-tree: an index for run-length compressed sequences
EDBT '08 Proceedings of the 11th international conference on Extending database technology: Advances in database technology
A new method for indexing genomes using on-disk suffix trees
Proceedings of the 17th ACM conference on Information and knowledge management
Serial and parallel methods for i/o efficient suffix tree construction
Proceedings of the 2009 ACM SIGMOD International Conference on Management of data
Suffix trees for very large genomic sequences
Proceedings of the 18th ACM conference on Information and knowledge management
Indexing genomic sequences on the IBM Blue Gene
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Suffix tree construction algorithms on modern hardware
Proceedings of the 13th International Conference on Extending Database Technology
Biochemical network matching and composition
Proceedings of the 2010 EDBT/ICDT Workshops
Fast construction of generalized suffix trees over a very large alphabet
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Efficient and scalable indexing techniques for biological sequence data
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
Exhaustive peptide searching using relations
BNCOD'07 Proceedings of the 24th British national conference on Databases
A hash trie filter method for approximate string matching in genomic databases
Applied Intelligence
I/O efficient algorithms for serial and parallel suffix tree construction
ACM Transactions on Database Systems (TODS)
Search-Optimized suffix-tree storage for biological applications
HiPC'05 Proceedings of the 12th international conference on High Performance Computing
Parallel construction of large suffix trees on a PC cluster
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
Indexing DNA sequences using q-grams
DASFAA'05 Proceedings of the 10th international conference on Database Systems for Advanced Applications
Efficient techniques on retrieving bio-information for active U-healthcare
Personal and Ubiquitous Computing
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