3D Phylogeny Explorer, a system for distinguishing paralogs and lateral transfer with 3D visualization, from the University of California, Los Angeles: www.bioinformatics.ucla.edu/3DPhylogenyExplorer.
ASViewer, a software package for visualizing the transcript structure and functional features of alternatively spliced variants, from EwhaWomansUniversity in South Korea http://genome.ewha.ac.kr/ASviewer/.
BioPostgres, a collection of modules that extend PostgreSQL for computational biology, from the Center for Computational Biology at the University of California, Los Angeles: http://www.biopostgres.org/.
BioTermNet, an automatic network-drawing system based on information retrieval and information extraction techniques, from the University of Tokyo: http://btn.ontology.ims.u-tokyo.ac.jp/.
b-src, a search engine for bioinformatics source code, from the Computational Biology Research Center at Japan’s National Institute of Advanced Industrial Science and Technology: http://b-src.cbrc.jp/.
CAPSULO (Calling Programs for Predicting Subcellular Location of Proteins), an integrative tool to predict protein subcellular location using 10 different subcellular location prediction programs, from the Swiss Institute of Bioinformatics: http://biosapiens.isb-sib.ch/capsulo.
Contralign 2 (CONditional TRAining for Protein Sequence Alignment), an extensible parameter-learning framework for protein pairwise sequence alignment based on pair conditional random fields, from StanfordUniversity: http://contra.stanford.edu/contralign/.
eSLDB (Eukaryotic Subcellular Localization Database), a database of protein subcellular localization annotation for eukaryotic organisms, from the University of Bologna: http://gpcr.biocomp.unibo.it/esldb/.
Filtrest 3D, a method for ranking protein models with fuzzy structural restraints, from the International Institute of Molecular and Cell Biology in Warsaw, Poland: http://filtrest3d.genesilico.pl/.
FUNC, a collection of four programs to analyze the over- and under-representation of data associated with genes or gene products, from the Max-Planck Institute for Evolutionary Anthropology: http://func.eva.mpg.de/.
FunCoup, a system for integrating data and analyzing biological networks in eukaryotes, from Stockholm University: www.sbc.su.se/~andale/funcoup.html.
GenePro, a Cytoscape plug-in for visualizing and analyzing interaction networks, from the Hospital for Sick Children: http://genepro.ccb.sickkids.ca/.
Ginga, (Graphical Interface for Comparative Genome Analysis), a system for comparative analysis between a bacterial genome sequence and that of a closely related bacterial species, from Brazil’s Laboratório Nacional de Computação Científica: http://www.ginga.lncc.br/.
Hollywood, a database of alternatively spliced mRNAs, from the Massachusetts Institute of Technology: http://hollywood.mit.edu/.
MadNet, representation of gene expression data on maps of cellular processes, protein networks and metabolic pathways, from the Department of Molecular Biology at the Division of Biology, Faculty of Science, in Zagreb, Croatia: http://bioinfo.hr/madnet.
Meta-MQAP, a meta-server based on support vector machines that assesses the quality of protein models, from the International Institute of Molecular and Cell Biology in Warsaw: https://genesilico.pl/toolkit/.
NQ-Flipper, a web service that recognizes “unfavorable” rotamers of Asn and Gln residues in protein structures, from the University of Salzburg: http://flipper.services.came.sbg.ac.at/.
Ontology of Functions, from the Max Planck Institute for Evolutionary Anthropology: http://onto.eva.mpg.de/onto_functions.html.
Probacter, a database of proteins from complete and publicly available proteomes of plant-associated bacteria, from Brazil’s Laboratório Nacional de Computação Científica: http://www.probacter.lncc.br/dhtml/index.cgi.
PropPred, a package for predicting the physico-chemical properties for small molecules, from the University of Alberta: http://hmdb.med.ualberta.ca/~eisner/PropPred/.
QGRS Mapper, a software program that generates information on composition and distribution of putative quadruplex-forming G-rich sequences, from Ramapo College: http://bioinformatics.ramapo.edu/QGRS/.
SNP Ontology, from LORIA (Laboratoire Lorrain de Recherche en Informatique et ses Applications): www.loria.fr/~coulet/ontology/snpontology.owl.
Sybil, a web-based software package for comparative genomics, from the Institute for Genomic Research: http://sybil.sourceforge.net/.
TreeDomViewer, a software tool for visualizing phylogeny and protein domain structure, from Wageningen University: www.bioinformatics.nl/tools/treedom/.
Twease, a web-based tool for searching Medline at the abstract level, from Weill Medical College of Cornell University: http://www.twease.org/.
UniHI, a tool for unifying large-scale maps of the human protein interactome, from Germany’s Institute for Theoretical Biology: www.mdc-berlin.de/unihi.
XMLPipeDB, an open source suite of Java-based tools for automatically building relational databases from an XML schema, from LoyolaMarymountUniversity: www.cs.lmu.edu/~xmlpipedb.
XXStout, a method for improving the prediction of long-range residue contacts, from University College Dublin: http://distill.ucd.ie/.
yrGate (Your Gene Structure Annotation Tool for Eukaryotes), an annotation tool and community utilities for web-based community gene annotation, from Iowa State University: www.plantgdb.org/prj/yrGATE.