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Software Tools

ParaBioSys-developed Software Tools:

Boston University

  • Cross-Genome Search and Analysis Tools
    The CGAn report generated by this link shows the top two homologues with at least 20% equivelent identities for each organism in our completed genomes set. It also reports any strong homology to a PDB structural sequence, if it's known to be a wd-repeat, if it is in the defining set of or had a domain identified by one of our profiles.

Harvard Medical School

  • AlignACE (Aligns Nucleic Acid Conserved Elements)
    A program that uses a motif-finding algorithm to find sequence elements conserved in a set of DNA sequences.
  • CompareACE
    A program to compare sequences to selected motifs in Saccharomyces cerevisiae.
  • ExpressDB
    A relational database containing yeast and E. coli RNA expression data. As of October, 2000 it contains more than 20 million pieces of information loaded from numerous published and in-house expression studies.
    A BLAST-based strategy using the Celera draft mouse genome assembly and the NCBI draft human genome assembly to define ~1.15 million "islands" of strong homology, covering the most conserved ~10% of each genome. These elements have been used to generate a "humanized" version of the mouse genome and a "mousenized" version of the human genome.
  • Masliner (MicroArray Spot LINEr Regression)
    Measuring absolute expression with microarrays using a calibrated reference sample and an extended signal intensity range.
  • NetSearch
    A computational approach for generating static models of signal transduction networks which utilizes protein-interaction maps generated from large-scale two-hybrid screens and expression profiles from DNA microarrays. Networks are determined entirely by integrating protein-protein interaction data with microarray expression data, without prior knowledge of any pathway intermediates.
  • Polony Technology and Software
    Image analysis for haplotyping, exon-typing and sequencing.

Massachusetts General Hospital

  • MGH-PGA BASE Plug-in Suite
    A number of plug-ins written for the BioArray Software Environment provide it with a greatly expanded ability to analyze microarray expression data.
  • MGH-PGA Proteomic Tools
    Our database is based on NCBI's protein database, with additional information about the DNA coding sequences. It allows identification of the DNA coding sequences by searching for peptide sequences. You may also upload a protein file and get the corresponding DNA coding sequences, as well as primers designed for PCR.
  • PrimerBank
    PrimerBank is a public resource for PCR primers. These primers are designed for gene-expression detection or quantification (real-time PCR). PrimerBank contains about 180,000 primers covering most known human and mouse genes.
  • OligoPicker
    OligoPicker selects up to five oligo probes for each of the DNA sequences you provide for microarray printing. OligoPicker picks specific oligos by skipping regions with contiguous bases common in other sequences. In addition, oligo specificity is double-checked by BLAST.
  • Oligo List Builder for Synthetic Genes
  • Web Map
    This program creates flexibly formatted sequence maps from a variety of inputs, including GenBank pages formatted as either text or html. The maps are hyperlinked to GenBank resources and present expository information through popup windows. A very large number of style options are available to display SNPs, open reading frames, and restriction enzyme cleavage sites.

Other Gene Expression Data Analysis Tools

  • BASE - BioArray Software Environment
    BASE is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis.
  • Eisen Lab ScanAlyze, Cluster, and Treeview.
    - ScanAlyze processes fluorescent images of microarrays. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database.
    - Cluster and TreeView are an integrated pair of programs for analyzing and visualizing the results of complex microarray experiments.
  • CyberT (Genex)
    Freeware. Data analysis tool.
  • Gene Micro-Array Pathway Profiler (GenMAPP) (Conklin lab, Gladstone Institutes)
    Freeware. Maps your gene expression data onto biological pathways. The program allows you to make your own pathways, or use archive pathways.
  • GeneCluster (Broad Institute)
    Freeware. Program for generating self-organizing maps.
  • GeneX (NCGR)
    Freeware. Data analysis tool.
  • MicroArray Suite (Affymetrix)
    Software that converts raw intensity readings from Affymetrix scanner into expression values.
  • NetAffx (Affymetrix)
    Online portal that allows you to search Affymetrix chips for genes of interest, download sequence files and link your experimental results to functional annotations.
  • Cluster and TreeView ( Stanford Genome Analysis Group)
    Freeware. Allows performance of Hierarchical clustering, K-means clustering and Self-organizing maps, while TreeView is used to view the results from Cluster.
  • GenePix Pro (Axon)
    Software that analyses intensities from Axon scanner and converts readings into Cy3/Cy5 ratios.
  • BRB ArrayTools
    Freeware. Excel plug-in that allows you to consolidate data from different files and also includes features such as clustering and scatter plots.
  • SAM
    Freeware. Supervised learning software for genomic expression data mining.
  • TIGR Software Tools include ArrayViewer, MultiExperiment Viewer, and Spotfinder.
    - TIGR ArrayViewer facilitates the presentation and analysis of microarray expression data, leading to the identification of genes that are differentially expressed.
    - TIGR MultiExperiment Viewer (MEV) is a Java application designed to allow the analysis of microarray data to identify patterns of gene expression and differentially expressed genes.
    - TIGR Spotfinder is designed for Microarray image processing using the TIFF image files generated by most microarray scanners.
  • UCSF Spot
    Freeware. A program for microarray image quantification. It is fully automatic, from the gridding process through ratio derivation.
  • XCluster (Stanford University)
    Freeware. Data analysis tool.

Repositories (Databases) of Gene Expression Data

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