Indexing genomic sequence libraries

This paper describes an extensible, open-source (GPL) data repository and retrieval system that supports fast, efficient, keyword based retrieval of genomic sequences from multiple libraries with retrieved sequences post-processed by FASTA, Smith-Waterman and other analysis software. This applicatio...

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Bibliographic Details
Published in:Information processing & management 2005-03, Vol.41 (2), p.265-274
Main Authors: O'KANE, Kevin C, LOCKNER, Matthew J
Format: Article
Language:English
Subjects:
Bioinformatics
Documentation institutions
Exact sciences and technology
Full text databases
Genomics
Information and communication sciences
Information retrieval
Information retrieval systems
Information retrieval systems. Information and document management system
Information science. Documentation
Libraries. Virtual and electronic libraries. Media centers. Documentation centers
Online databases
Online information retrieval
Research and special libraries
Sciences and techniques of general use
Searching
Studies
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Summary:This paper describes an extensible, open-source (GPL) data repository and retrieval system that supports fast, efficient, keyword based retrieval of genomic sequences from multiple libraries with retrieved sequences post-processed by FASTA, Smith-Waterman and other analysis software. This application is implemented for Linux and is written in Mumps, C, and C++ with supporting components that include the Berkeley Data Base, the Perl Compatible Regular Expression Library, GLADE, and tools such as FASTA, Smith-Waterman, and modules from EMBOSS. The package described here can quickly index data sets of up to 256 terabytes using a B-tree based multi-dimensional data model. An example is presented that indexes the text of the full NCBI Genbank library. [PUBLICATION ABSTRACT]
ISSN:0306-4573
1873-5371
DOI:10.1016/j.ipm.2003.09.001