title: An integrated web interface for large-scale characterization of sequence data.
abstract: Large-scale genome projects require the analysis of large amounts of raw data. This analysis often involves the application of a chain of biology-based programs. Many of these programs are difficult to operate because they are non-integrated, command-line driven, and platform-dependent. The problem is compounded when the number of data files involved is large, making navigation and status-tracking difficult. To demonstrate how this problem can be addressed, we have created a platform-independent Web front end that integrates a set of programs used in a genomic project analyzing gene function by transposon mutagenesis in Saccharomyces cerevisiae. In particular, these programs help define a large number of transposon insertion events within the yeast genome, identifying both the precise site of transposon insertion as well as potential open reading frames disrupted by this insertion event. Our Web interface facilitates this analysis by performing the following tasks. Firstly, it allows each of the analysis programs to be launched against multiple directories of data files. Secondly, it allows the user to view, download, and upload files generated by the programs. Thirdly, it indicates which sets of data directories have been processed by each program. Although designed specifically to aid in this project, our interface exemplifies a general approach by which independent software programs may be integrated into an efficient protocol for large-scale genomic data processing.
authors.affiliation: Center for Medical Informatics, Yale University School of Medicine, 333 Cedar Street, P.O. Box 208009, New Haven, CT 06520-8009, USA. kei.cheung@yale.edu
authors.forename: K H
authors.initials: KH
authors.lastname: Cheung
authors.forename: A
authors.initials: A
authors.lastname: Kumar
authors.forename: M
authors.initials: M
authors.lastname: Snyder
authors.forename: P
authors.initials: P
authors.lastname: Miller
mesh_terms: D002984:Clinical Laboratory Information Systems; D019295:Computational Biology / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D030541:Databases, Genetic; D030562:Databases, Protein; D020869:Gene Expression Profiling; D016678:Genome; D016681:Genome, Fungal; D020407:Internet; D016254:Mutagenesis, Insertional; D016366:Open Reading Frames; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface
chemical_list: D004251:DNA Transposable Elements; D004271:DNA, Fungal