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GeneCluster, eGenome, Gene Construction Kit, IPI


The Cancer Genomics Group at the Whitehead Institute Center for Genome Research has released version 2.0 of its GeneCluster gene expression analysis application. The new release adds several features, including more options for pre-processing, marker selection, supervised classification, multiclass prediction, permutation test methods, and visualization.

GeneCluster 2.0 provides a gene marker selector based on neighborhood analysis, permutation tests, and visualization that allows users to view, sort, and color-code their data by keyword. It also includes tools for building supervised models using weighted voting and k-nearest neighbor algorithms. A beta version of the software, which can also be used for proteomic data, is available for free at


A beta version of eGenome — a position-based catalog of transcripts, markers, polymorphisms, large-insert clones, and DNA sequences for the human genome — is available from the Children’s Hospital of Philadelphia at A stable site with up-to-date content is expected to launch in July.


SciQuest of Research Triangle Park, NC, has released version 2.5 of its Gene Construction Kit, a DNA manipulation, cloning design, and illustration tool.

Enhancements in version 2.5 include a deluxe importer module that allows users to import GenBank and EMBL data and a customizable interface that converts GenBank and EMBL features to graphical GCK features. The software has also been ported to Mac OS X.


An IPI (International Protein Index) set is now available for mouse from the European Bioinformatics Institute at

The mouse IPI is a non-redundant protein set assembled from mouse sequences in Ensembl, SwissProt, Trembl, and RefSeq. Version 1.0 of the mouse IPI contains 30,517 sequences.

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The Scan

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.

Circulating Tumor DNA Shows Potential as Biomarker in Rare Childhood Cancer

A study in the Journal of Clinical Oncology has found that circulating tumor DNA levels in rhabdomyosarcoma may serve as a biomarker for prognosis.

Study Recommends Cancer Screening for Dogs Beginning Age Seven, Depending on Breed

PetDx researchers report in PLOS One that annual cancer screening for dogs should begin by age seven.

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.