A sequence comparison and gene expression data integration add-on for the Pathway Tools software

• Published in: Bioinformatics 2012-09, Vol.28 (17), p.2283-2284
• Main Authors: KREMPL, Peter M, MAIRHOFER, Juergen, STRIEDNER, Gerald, THALLINGER, Gerhard G
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; Databases, Genetic; DNA Transposable Elements; Fundamental and applied biological sciences. Psychology; Gene Expression; Gene Expression Profiling - methods; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Annotation; Sequence Alignment; Sequence Homology, Nucleic Acid; Software
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/bts431

We present a plug-in for Pathway Tools, an integrated systems biology software to create, maintain and query Pathway/Genome Databases. Fully integrated into the graphical user interface and menu, this plug-in extends the application's functionality by the ability to create multiple sequence alignments, systematically annotate insertion sequence (IS) elements and analyse their activity by cross-species comparison tools. Microarray probes can be automatically mapped to target genes, and expression data obtained with these arrays can be transformed into input formats needed to visualize them in the various omics viewers of Pathway Tools. The plug-in API itself allows developers to integrate their own functions into the Pathway Tools menu. Binaries are freely available for non-commercial users at http://genome.tugraz.at/PGDBToolbox/ and can be used on all platforms supported by Pathway Tools. A user guide is freely available at: http://genome.tugraz.at/PGDBToolbox/documentation.shtml.