MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer.

Maturation of eukaryotic pre-mRNAs via splicing and polyadenylation is modulated across cell types and conditions by a variety of RNA-binding proteins (RBPs). Although there exist over 1,500 RBPs in human cells, their binding motifs and functions still remain to be elucidated, especially in the complex environment of tissues and in the context of diseases. To overcome the lack of methods for the systematic and automated detection of sequence motif-guided pre-mRNA processing regulation from RNA sequencing (RNA-Seq) data we have developed MAPP (Motif Activity on Pre-mRNA Processing).

Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords.

Due to their nature, bioinformatics datasets are often closely related to each other. For this reason, search, mapping and visualization of these relations are often performed manually or programmatically via identifiers or special keywords such as gene symbols. Although various tools exist for these situations, the growing volume of bioinformatics datasets, emerging new software tools and approaches motivates new solutions.

The EMBL-EBI search and sequence analysis tools APIs in 2019.

The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.

The EBI search engine: EBI search as a service-making biological data accessible for all.

We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include nucleotide and protein sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, as well as the life science literature. EBI Search provides a powerful RESTful API that enables its integration into third-party portals, thus providing 'Search as a Service' capabilities, which are the main topic of this article.

The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI.

The European Bioinformatics Institute (EMBL-EBI-https://www.ebi.ac.

The EMBL-EBI bioinformatics web and programmatic tools framework.

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.

Assembly information services in the European Nucleotide Archive.

The European Nucleotide Archive (ENA; http://www.ebi.ac.