MOTIVATION: Identification and interpretation of clinically actionable variants is a critical bottleneck. Searching for evidence in the literature is mandatory according to ASCO/AMP/CAP practice guidelines; however, it is both labor-intensive and error-prone. We developed a system to perform triage of publications relevant to support an evidence-based decision. The system is also able to prioritize variants. Our system searches within pre-annotated collections such as MEDLINE and PubMed Central. RESULTS: We assess the search effectiveness of the system using three different experimental settings: literature triage; variant prioritization and comparison of Variomes with LitVar. Almost two-thirds of the publications returned in the top-5 are relevant for clinical decision-support. Our approach enabled identifying 81.8% of clinically actionable variants in the top-3. Variomes retrieves on average +21.3% more articles than LitVar and returns the same number of results or more results than LitVar for 90% of the queries when tested on a set of 803 queries; thus, establishing a new baseline for searching the literature about variants. AVAILABILITY AND IMPLEMENTATION: Variomes is publicly available at https://candy.hesge.ch/Variomes. Source code is freely available at https://github.com/variomes/sibtm-variomes. SynVar is publicly available at https://goldorak.hesge.ch/synvar. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: The Feature-Viewer is a lightweight library for the visualization of biological data mapped to a protein or nucleotide sequence. It is designed for ease of use while allowing for a full customization. The library is already used by several biological data resources and allows intuitive visual mapping of a full spectra of sequence features for different usages. AVAILABILITY AND IMPLEMENTATION: The Feature-Viewer is open source, compatible with state-of-the-art development technologies and responsive, also for mobile viewing. Documentation and usage examples are available online.

SUMMARY: The neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants. AVAILABILITY AND IMPLEMENTATION: The pepx program is available at https://github.com/calipho-sib/pepx and can be launched from the command line or through a cgi web interface. Indexing requires a sequence file in FASTA format. The peptide uniqueness checker tool is freely available on the web at https://www.nextprot.org/tools/peptide-uniqueness-checker and from the neXtProt API at https://api.nextprot.org/. CONTACT: [email protected].