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Xpression NTI, STACKdb, GeneSpring


InforMax of Bethesda, Md., has released a new desktop application for the analysis of gene expression data, Xpression NTI, as well as the latest upgrade to its Vector NTI Suite.

Xpression NTI provides a variety of algorithms for the processing and analysis of data from single and multiple microarray expression experiments. Filtering, sorting, clustering, parameterization, or profiling methods can be used to analyze and organize data.

Version 7.0 of the Vector NTI sequence analysis and data management software package offers increased functionality across all of the suite application programs — Vector NTI, AlignX, BioPlot, and ContigExpress. According to InforMax, notable enhancements include optimized recombinant strategies and protocols, enhanced primer design and analysis capabilities, an enhanced Blast viewer for customized visualization of sequence data, and improved utilities for sequence alignment and contig assembly.


Electric Genetics and the South African National Bioinformatics Institute have released version 3.0 of the STACKdb human gene expression index. The latest version incorporates mRNA sequences and web-based visualization software.

STACKdb v3.0 offers an increase of 569,014 new EST sequences and 51,638 mRNA sequences over STACKdb v2.4. The database is now distributed in two forms: relational database tables, for use with the viewing software, and FastA files for use with external programs.

Academic and non-profits may register at to download STACKdb v3.0.


Silicon Genetics, based in Redwood City, Calif., will now market the ArrayMiner clustering algorithm from Brussels-based Optimal Design for use with its GeneSpring gene expression analysis software. ArrayMiner uses genetic algorithms to cluster gene expression data.

Silicon Genetics is offering an evaluation of ArrayMiner through


Alexander Kozik of the Department of Vegetable Crops at the University of California at Davis has made PhyloGrapher — a program designed to visualize and study evolutional relationships between families of homologous genes or proteins — freely available at

PhyloGrapher is a drawing tool that generates custom graphs out of the given set of genes.

Biobase of Wolfenb¸ttel, Germany, has released Cytomer, a database describing a hierarchical classification structure for physiological systems, organs, and cell types. According to Biobase, Cytomer can be used to map gene expression data to its expression sources.


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The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

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