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Scriptable Access to the Caenorhabditis elegans Genome Sequence and Other ACEDB Databases

Authors
Publisher
Cold Spring Harbor Laboratory Press
Publication Date
Source
PMC
Keywords
  • Methods
Disciplines
  • Biology
  • Computer Science

Abstract

Much of the world’s genomic data are available to the community through networked databases that are accessed via Web interfaces. Although this paradigm provides browse-level access and has greatly facilitated linking between databases, it does not provide any convenient mechanism for programmatically fetching and integrating data from diverse databases. We have created a library and an application programming interface (API) named AcePerl that provides simple, direct access to ACEDB databases from the Perl programming language. With this library, programmers and computer-savvy biologists can write software to pose complex queries on local and remote ACEDB databases, retrieve the data, integrate the results, and move data objects from one database to another. In addition, a set of Web scripts running on top of AcePerl provides Web-based browsing of any local or remote ACEDB database. AcePerl and the AceBrowser Web browser run on Unix systems and are available under a license that allows for unrestricted use and redistribution. Both packages can be downloaded from URL http://stein.cshl.org/AcePerl. A Microsoft Windows port of AcePerl is in the planning stages.

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