Genome Explorer is the central module enabling in-depth analysis of proprietary and public genomes. Designed for scalability, thousands of prokaryotic and eukaryotic genomes can be collectively investigated. Genome Explorer offers intuitive graphical browsers and sequence analysis programs which facilitate tasks such as comparative genomics, while data management tools update and extend functional gene annotation.

Mutation Explorer analyzes genomes of microbial production strains and their derivatives to identify SNPs, insertions, deletions, and more complex genetic polymorphisms and variants. The module facilitates genome-wide analysis of strain genotypes and correlates mutations as well as complex mutation patterns with specific strain phenotypes. Developed specifically for managing and interpreting large and complex genetic studies using next-generation sequencing technologies, Mutation Explorer enables identification of biomarkers which can be used to predict strain performance.

Pathway Explorer enables the storage and analysis of public and proprietary pathway data. The module contains tools for pathway activation analyses with transcriptomic, proteomic, and metabolomic profiling data in the context of specific pathways. Pathway Explorer also performs cross-organism pathway analyses to identify the most suitable strain for experimentation to test functional hypotheses and to perform strain optimization studies.

The Sequence Data Center (SDC) is dedicated to the secure behind-the-firewall management of proprietary and public sequence data (including sequence annotation). A comprehensive suite of software agents available for all major data repositories automatically update relevant content. Specifically designed for the storage of many millions of sequences, the SDC is extremely scalable as well as extendable.

Sequence Explorer provides a comprehensive integration platform including all major protein and nucleic acid sequence analysis programs such as BLAST, ClustalW, Pfam, and the EMBOSS suite. Sequence Explorer is easily extended with other public sequence analysis tools or proprietary in-house programs. All results are saved to the Selector database and can be analyzed interactively with powerful graphical programs.

Expression Explorer enables the investigation of gene expression data (e.g. from all major next-generation sequencing as well as microarray platforms) in a broader biological context. The module allows visualization of genes corresponding, for example, to a list of co-regulated probe sets derived from molecular profiling studies in the context of gene location and generates gene-centric views of key profiling data across multiple samples (‘electronic Northern’).

Signaling Explorer focuses on the storage and analysis of signaling pathway data. By integrating data from different public and commercial sources, it enables the generation of super-pathways based on different data content. It models arbitrary molecules and events such as compounds, promoters, co-factors, enzymatic reactions, or post-translational modifications in different cellular compartments, overlays molecular profiling data on signaling pathways, and extends pathways to capture the latest knowledge in the field.

Promoter Explorer enables the integrated storage and analysis of promoter and regulatory network data. It facilitates the genome-wide analysis of transcription control mechanisms and specifically helps to predict target genes of individual transcription factors. It includes tools that integrate experimental data (e.g., ChIP-chip, validated miRNA targets), compare data with computational predictions (generated e.g., from PWM-based approaches), and investigate promoter architectures. These capabilities help to answer critical questions, such as which transcription factors account for co-regulation of a group of genes, or whether transcriptional control is conserved in a group of orthologs.

Literature Explorer facilitates the storage and querying of scientific literature and other document-based findings. Scientific articles (e.g. PubMed) link to relevant biological entities including genes, proteins, transcription factors, pathways, and more. Literature explorer enables workflows such as retrieval of all genes with a specific phenotype relation in all available literature.

Patent Explorer stores and analyzes bio-molecule patent information. It enables interdisciplinary collaboration among scientists, patent lawyers, and project and business managers so that targets are evaluated from both intellectual property and biological standpoints. Advancing decision-making based on competitive data in specific research areas and filing and priority dates, Patent Explorer drives scientifically sound early-stage target identification, which is free of competing intellectual property claims.

The specialized high-level Xtend API integrates complex software systems and allows Genedata Selector to dynamically pull and appropriately display relevant data from all kinds of database systems. The module facilitates gene-centric organization of all gene-related information including molecular profiling and phenotype data. Xtend API also facilitates portfolio and project database integration and customization of the Selector user interface.