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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.
- HUMMUS
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
General Information
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