Gbench (NCBI Genome Workbench) is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.
cddApp is a Cytoscape3 extension that supports the annotation of protein networks with information about domains and specific functional sites (features) from the National Center for Biotechnology Information (NCBI) Conserved Domain Database (CDD).
RefSeq (the Reference Sequence) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq is a foundation for medical, functional, and diversity studies; they provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.
ProMatch is a Java-based standalone program to match input parameters such as peptide and mRNA sequences to entries in NCBI Reference Sequence Database (RefSeq). ProMatch helps identify and eliminate ambiguous identifications from proteomic and transcriptomic data.
GEOquery effectively establishes a bridge between GEO and BioConductor. Easy access to GEO data from BioConductor will likely lead to new analyses of GEO data using novel and rigorous statistical and bioinformatic tools.
Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest.