ABSTRACT
The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the database has grown by an order of magnitude over the previous version and now includes 100 species and their collective 1.3 million proteins organized into 42.7 million pairwise ortholog groups. The InParanoid algorithm itself has been revised and is now both more specific and sensitive. Based on results from our recent benchmarking of low-complexity filters in homology assignment, a two-pass BLAST approach was developed that makes use of high-precision compositional score matrix adjustment, but avoids the alignment truncation that sometimes follows. We have also updated the InParanoid web site (http://InParanoid.sbc.su.se). Several features have been added, the response times have been improved and the site now sports a new, clearer look. As the number of ortholog databases has grown, it has become difficult to compare among these resources due to a lack of standardized source data and incompatible representations of ortholog relationships. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters.
Subject(s)
Computational Biology/methods , Databases, Genetic , Databases, Nucleic Acid , Escherichia coli/genetics , Eukaryotic Cells/chemistry , Proteins/genetics , Algorithms , Animals , Cluster Analysis , Computational Biology/trends , Escherichia coli/metabolism , Genome, Bacterial , Humans , Information Storage and Retrieval/methods , Internet , Protein Structure, Tertiary , Proteomics/methods , SoftwareABSTRACT
Molecular dynamics (MD) is a technique to simulate movements of molecular structures to understand their functional behavior. GROMACS is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. This makes it powerful but also complicated to handle. We introduce jSimMacs, a Java application for creating molecular dynamics projects in GROMACS. It simplifies the handling of files and options via an intuitive user interface. Users unexperienced in MD can work along prepared lines, while experts may enjoy a significant relief from the tedium of typing and scripting. Furthermore, jSimMacs supports 3D interactivity and the launch of remote projects on other computers accessible via networks. Thus, jSimMacs not only opens GROMACS to a broader public but also eases the burden of performing series of MD runs, as necessary in parameter studies.
Subject(s)
Molecular Dynamics Simulation , Software , Computer Graphics , User-Computer InterfaceABSTRACT
UNLABELLED: jSquid is a graph visualization tool for exploring graphs from protein-protein interaction or functional coupling networks. The tool was designed for the FunCoup web site, but can be used for any similar network exploring purpose. The program offers various visualization and graph manipulation techniques to increase the utility for the user. AVAILABILITY: jSquid is available for direct usage and download at http://jSquid.sbc.su.se including source code under the GPLv3 license, and input examples. It requires Java version 5 or higher to run properly. CONTACT: erik.sonnhammer@sbc.su.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
