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FinchLab, ExpressionCorrelation, RDP 10.4

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Geospiza has released an upgrade for its FinchLab software, which includes “significant analysis enhancements” for second-generation sequencing, the company said.
 
The current release supports tag profiling, resequencing, transcriptomes, and ChIP-seq analysis pipelines for the Illumina Genome Analyzer and tag profiling and transcriptome analysis pipelines for Applied Biosystems SOLiD instruments.
 
There are also “substantial improvements’ for Roche 454 workflows and many aspects of the lab management system. The next release, planned for November, will include additional analysis capabilities for SOLiD and Roche 454, the company said.
 

 
Developers at Memorial Sloan-Kettering Cancer Center and the University of Toronto have released a new Cytoscape plug-in called ExpressionCorrelation, which creates a network from gene expression data.
 
It computes a similarity network from either the genes or conditions in a gene expression matrix. The nodes in the similarity network represent genes or conditions and the edges represent the similarity between vectors of the expression levels of genes across all given conditions, in the case of a gene correlation network, or the similarity between vectors of the expression levels of all genes in a single condition, in the case of a condition correlation network.
 
The plug-in allows users to select an expression matrix of microarray data directly from Cytoscape, computes the similarity matrix using the Pearson correlation coefficient, and converts it to an interaction network in Cytoscape.
 

 
The Ribosomal Database Project hosted at Michigan State University has released RDP 10, Update 4.
 
RDP provides ribosome-related data and services to the scientific community, including online data analysis and aligned and annotated bacterial and archaeal small-subunit 16S rRNA sequences.
 
Release 10.4 contains 690,149 aligned 16S rRNA sequences. It brings two major changes: new bacterial and archaeal alignments with enhancements over the previous RDP 9 alignments.
 
Also, the Infernal secondary-structure based aligner provides “better support” for short partial sequences and handles certain sequencing artifacts in a “more intuitive manner,” according to a release. 

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