Faculty Publications

Indexing Genomic Sequence Libraries

Document Type

Article

Keywords

Bioinformatics, Genomics, Information retrieval, Mumps, Sequence retrieval

Journal/Book/Conference Title

Information Processing and Management

Volume

41

Issue

2

First Page

265

Last Page

274

Abstract

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. © 2003 Elsevier Ltd. All rights reserved.

Department

Department of Computer Science

Original Publication Date

3-1-2005

DOI of published version

10.1016/j.ipm.2003.09.001

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