Summary: Software application for retrieving, presenting and traversing information resources on the World Wide Web.
- Ciemny M, Kurcinski M, Kozak K, Kolinski A, Kmiecik S. Highly Flexible Protein-Peptide Docking Using CABS-Dock. Methods Mol Biol. 2017;1561:69-94 pubmed publisher..Finally, a tutorial for running CABS-dock from the command line or command line scripts is provided. The CABS-dock web server is available from http://biocomp.chem.uw.edu.pl/CABSdock/ . ..
- Ponyared P, Ponsawat J, Tongsima S, Seresangtakul P, Akkasaeng C, Tantisuwichwong N. ESAP plus: a web-based server for EST-SSR marker development. BMC Genomics. 2016;17:1035 pubmed publisher..ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/ . ..
- . Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res. 2017;45:D331-D338 pubmed publisher..To learn more, visit http://geneontology.org/. ..
- Tang Z, Bunn P, Tao R, Liu Z, Lin D. PreMeta: a tool to facilitate meta-analysis of rare-variant associations. BMC Genomics. 2017;18:160 pubmed publisher..PreMeta processes summary statistics from the four packages to make them compatible and avoids the need to redo study-level analyses. PreMeta documentation and executable are available at: http://dlin.web.unc.edu/software/premeta . ..
- Russo F, Di Bella S, Bonnici V, Laganà A, Rainaldi G, Pellegrini M, et al. A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs. BMC Genomics. 2014;15 Suppl 3:S4 pubmed publisher..This allows users to improve the knowledge about the function, diagnostic potential, and the drug effects on cellular and circulating miRNAs. ..
- Van Bel M, Proost S, Van Neste C, Deforce D, Van de Peer Y, Vandepoele K. TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Genome Biol. 2013;14:R134 pubmed publisher..Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/. ..
- Tun S, Lubell Y, Dondorp A, Fieldman T, Tun K, Celhay O, et al. Identifying artemisinin resistance from parasite clearance half-life data with a simple Shiny web application. PLoS ONE. 2017;12:e0177840 pubmed publisher..falciparum infected patients after treatment with artemisinin derivatives, so that resistance to artemisinin can be identified. The tool can be accessed at bit.ly/id_artemisinin_resistance. ..
- Ferdman S, Minkov E, Bekkerman R, Gefen D. Quantifying the web browser ecosystem. PLoS ONE. 2017;12:e0179281 pubmed publisher..Results may herald insight on how other evolving internet ecosystems may behave, and suggest a methodology for measuring this behavior. Specifically, applying such a methodology could transform the addon market. ..
- Coletta A, Molter C, Duque R, Steenhoff D, Taminau J, de Schaetzen V, et al. InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor. Genome Biol. 2012;13:R104 pubmed publisher..The InSilico DB platform is a powerful collaborative environment, with advanced capabilities for biocuration, dataset sharing, and dataset subsetting and combination. InSilico DB is available from https://insilicodb.org. ..
- . UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45:D158-D169 pubmed publisher..We provide a SPARQL endpoint that allows complex queries of the more than 22 billion triples of data in UniProt (http://sparql.uniprot.org/). UniProt resources can be accessed via the website at http://www.uniprot.org/. ..
- Mutarelli M, Marwah V, Rispoli R, Carrella D, Dharmalingam G, Oliva G, et al. A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders. BMC Genomics. 2014;15 Suppl 3:S5 pubmed publisher..This resource may become a valuable tool to help dissecting the genotype underlying the disease phenotype through an improved selection of putative patient-specific causative or phenotype-associated variations. ..
- Lee B, Tiong K, Chang J, Liew C, Abdul Rahman Z, Tan A, et al. DeSigN: connecting gene expression with therapeutics for drug repurposing and development. BMC Genomics. 2017;18:934 pubmed publisher..This user-friendly platform could be used to identify drugs with unanticipated efficacy against cancer cell lines of interest, and therefore could be used for the repurposing of drugs, thus improving the efficiency of drug development. ..
- Mallona I, Peinado M. Truke, a web tool to check for and handle excel misidentified gene symbols. BMC Genomics. 2017;18:242 pubmed publisher..following user's preferences. Truke is a data format conversion tool with a unique corrupted gene symbol detection utility. Truke is freely available without registration at http://maplab.cat/truke . ..
- Cheng X, Xiao X, Chou K. pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC. Gene. 2017;628:315-321 pubmed publisher..jci-bioinfo.cn/pLoc-mVirus/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. ..
- Qiao Y, Quinlan A, Jazaeri A, Verhaak R, Wheeler D, Marth G. SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol. 2014;15:443 pubmed publisher..SubcloneSeeker is available at: https://github.com/yiq/SubcloneSeeker. ..
- Xu Z, Liu J, Ni W, Peng Z, Guo Y, Ye W, et al. GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii). Database (Oxford). 2017;2017: pubmed publisher..http://www.grtedb.org/. ..
- Madden S, Clarke C, Gaule P, Aherne S, O Donovan N, Clynes M, et al. BreastMark: an integrated approach to mining publicly available transcriptomic datasets relating to breast cancer outcome. Breast Cancer Res. 2013;15:R52 pubmed..The value of this tool will be in the preliminary assessment of putative biomarkers in breast cancer. It will be of particular use to research groups with limited bioinformatics facilities. ..