SCRIPTABLE ACCESS TO THE C. elegans GENOME SEQUENCE AND OTHER ACEDB DATABASES

¹ Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 USA

² CNRS, CRBM and Physique Mathematique, Montpellier, France

Much of the world's genomic data is available to the community via 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 programmer's interface (API) named "AcePerl", that provides simple, direct access to ACEDB databases under 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 planned.