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BioInform s Surfing Report: Web-Based Tools from Genome Informatics 2005


Ergatis, from TIGR, is a genome annotation pipeline platform:

EvoPrinter, from the National Institute of Neurological Disorders and Stroke, is a comparative genomics tool that enables users to identify conserved DNA sequences in the context of a single species of interest:

ExonScan, from the Massachusetts Institute of Technology, predicts splice sites for vertebrate genomes:

Flash GViewer, from the Medical College of Wisconsin, is a customizable Flash movie that can be inserted into a web page to display chromosomes in a genome along with the locations of individual features on the chromosomes:

Galaxy, from the Penn State Center for Comparative Genomics and Bioinformatics, enables developers to easily create an HTML user interface for their data analysis tools:

GeneSeer, from Cold Spring Harbor Lab, is a name-translation database that enables researchers to reconcile gene names from different species:

HapMart, from Cold Spring Harbor Laboratory, is a data-mining interface for data from the International HapMap project:

NestedMICA, from the Wellcome Trust Sanger Institute, is a motif finder with applications in finding candidate transcription factor binding sites:

ProteinPathGrep, from Princeton University, finds all paths in a protein-protein interaction network that match a given pattern:

Sombrero, from the National University of Ireland, Galway, finds transcription factor binding sites by using a self-organizing map to find overrepresented motifs in a set of DNA sequences:

Sybil, from the Institute for Genomic Research, offers comparative analysis tools for TIGR's Pathema database of pathogenic genome sequences:

TreeFam, (tree families database), from the Wellcome Trust Sanger Institute, is a database of phylogenetic trees of animal genes:

Ulysses, from the University of British Columbia, can project molecular interaction networks across species in order to annotate human genes based on gene interactions in model organisms:

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