Indexing and Retrieval for Genomic Databases
IEEE Transactions on Knowledge and Data Engineering
Database indexing for large DNA and protein sequence collections
The VLDB Journal — The International Journal on Very Large Data Bases
Indexing Nucleotide Databases for Fast Query Evaluation
EDBT '96 Proceedings of the 5th International Conference on Extending Database Technology: Advances in Database Technology
FLASH: A Fast Look-Up Algorithm for String Homology
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
Efficient Index Structures for String Databases
Proceedings of the 27th International Conference on Very Large Data Bases
A Database Index to Large Biological Sequences
Proceedings of the 27th International Conference on Very Large Data Bases
The Design and Implementation of a Sequence Database System
VLDB '96 Proceedings of the 22th International Conference on Very Large Data Bases
Fast Filter-and-Refine Algorithms for Subsequence Selection
IDEAS '02 Proceedings of the 2002 International Symposium on Database Engineering & Applications
Indexing Genomic Databases for Fast Homology Searching
DEXA '02 Proceedings of the 13th International Conference on Database and Expert Systems Applications
Efficient querying on genomic databases by using metric space indexing techniques
DEXA '97 Proceedings of the 8th International Workshop on Database and Expert Systems Applications
Filtration of String Proximity Search via Transformation
BIBE '03 Proceedings of the 3rd IEEE Symposium on BioInformatics and BioEngineering
Effective Indexing and Filtering for Similarity Search in Large Biosequence Databases
BIBE '03 Proceedings of the 3rd IEEE Symposium on BioInformatics and BioEngineering
Efficient Subsequence Matching in Time Series Databases Under Time and Amplitude Transformations
ICDM '03 Proceedings of the Third IEEE International Conference on Data Mining
Variable-length intervals in homology search
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
An IDC-based Algorithm for Efficient Homology Filtration with Guaranteed Seriate Coverage
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
Efficient Filtration of Sequence Similarity Search Through Singular Value Decomposition
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
Brief communication: An efficient similarity search based on indexing in large DNA databases
Computational Biology and Chemistry
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Up to now, there are many homology search algorithms that have been investigated and studied. However, a good classification method and a comprehensive comparison for these algorithms are absent. This is especially true for index based homology search algorithms. The paper briefly introduces main index construction methods. According to index construction methods, index based homology search algorithms are classified into three categories, i.e., length based index ones, transformation based index ones, and their combination. Based on the classification, the characteristics of the currently popular index based homology search algorithms are compared and analyzed. At the same time, several promising and new index techniques are also discussed. As a whole, the paper provides a survey on index based homology search algorithms.