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Compression of nucleotide databases for fast searching

H Williams¹, J Zobel

¹Department of Computer Science, RMIT, Melbourne, Australia. hugh@cs.rmit.edu.au

Computer Applications in the Biosciences : CABIOS

|November 21, 1997

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A new direct coding scheme offers lossless compression and faster retrieval for genomic nucleotide databases. This method improves search times for homology searches, making large sequence databases more efficient.

Area of Science:

Bioinformatics
Genomic Data Management
Computational Biology

Background:

International sequencing initiatives generate vast nucleotide databases.
Efficient storage and rapid retrieval are critical for sequence homology search applications.
Disk I/O bottlenecks frequently impede the performance of large-scale sequence database searches.

Purpose of the Study:

To develop a novel direct coding scheme for genomic nucleotide data.
To achieve fast data retrieval and effective compression.
To enhance the efficiency of sequence search tools.

Main Methods:

Implementation of a purpose-built direct coding scheme.
Integration with existing sequence search tools.
Evaluation of compression ratios and retrieval speeds.

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Main Results:

The direct coding scheme provides lossless compression of genomic data.
Achieved faster data retrieval compared to uncompressed and other compressed methods.
Demonstrated significant improvements in search times for high-speed homology searches.

Conclusions:

The direct coding scheme is a viable solution for efficient genomic data storage and retrieval.
This approach offers practical benefits for large-scale bioinformatics applications.
The method enhances the performance of homology search tools.