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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:

Filed under

The Scan

And Back

The New York Times reports that missing SARS-CoV-2 genome sequences are back in a different database.

Lacks Family Hires Attorney

A lawyer for the family of Henrietta Lacks plans to seek compensation from pharmaceutical companies that have used her cancer cells in product development, the Baltimore Sun reports.

For the Unknown

The Associated Press reports that family members are calling on the US military to use new DNA analysis techniques to identify unknown sailors and Marines who were on the USS Arizona.

PLOS Papers on Congenital Heart Disease, COVID-19 Infection Host MicroRNAs, Multiple Malformation Mutations

In PLOS this week: new genes linked to congenital heart disease, microRNAs with altered expression in COVID-19, and more.