The MisPred database is a collection of protein sequences identified by the MisPred pipeline as erroneous (incomplete, abnormal or mispredicted). The MisPred database may be searched in various ways and you may also analyze your sequence using the MisPred pipeline to decide whether your sequence violates some basic rules of protein sequences.
Open Biological and Biomedical Ontologies, a collection of freely available well-structured controlled vocabularies.
Sandrine Palcy's insight:
The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. The groups developing ontologies who have expressed an interest in this goal are listed below, followed by other relevant efforts in this domain.
WGRV enables users to query databases containing pre-computed genome coordinates of evolutionarily conserved transcription factor binding sites in the proximal promoters (from 100 bp up to 5kb upstream) of human, mouse and Drosophila genomes. TF binding sites are based on position weight matrices from the TRANSFAC Professional database. For a given set of coregulated genes WGRV returns statistically enriched and evolutionarily conserved binding sites, mapped by the rVISTA (Regulatory VISTA) algorithm. Users can then retrieve a list of genes from the query set containing the enriched TF binding sites and their location in the query set promoters.
A new software platform called Sigpep that analyses transition redundancy in selected reaction monitoring (SRM) assays. Building on this platform, we also created a web application to generate transition sets with unique signatures for targeted peptides.
neXtProt, an on-line knowledge platform centered on human proteins. This exceptional resource provides life scientists with a broad spectrum of information on all human proteins via an intuitive interface. neXtProt is expected to become the central resource for any life scientist who requires high-quality information on human proteins in the context of modern biomedical research.
Network Data Integration, Analysis, and Visualization in a Box
Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
miRNAs have became a hot topic in biomedical sciences, because of their implications in several cellular processes ranging from differentiation to cancer. This page is a compilation of several tools to analyze miRNA sequences, determine their targets and to analyze their possible roles in cellular metabolism. The user can follow TUTORIALS that show how to extract information on miRNA function by using real and theoretical examples.
BioUML is open source integrated Java platform for building virtual cell and virtual physiological human. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses.