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General Links |
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WSU Bioinformatics |
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Washington
State University Bioinformatics Homepage—Data, software,
links, and support for the bioinformatics needs at Washington
State University |
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Biohealthmatics.com |
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Biohealthmatics.com—Comprehensive
website for Bio and Medical informatics topics and resources
such as academic and professional organizations, white papers
and reports, and a large selection of general information
and book selections |
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Dictionary of Cell Biology |
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The
Dictionary of Cell and Molecular Biology—Useful resource
for looking up dictionary listings of most things related
to cell and/or molecular biology including technologies
and techniques, gene families, individual genes, and cellular
functions |
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NCBI |
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National
Center for Biotechnology Information Homepage—Search
PubMed and GenBank, access bioinformatics, sequence, organism,
and technology information and public databases from this
well known source created by NIH |
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PubCrawler |
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An
Update and Alerting Service for PubMed and GenBank—Sign
up for free customizable emails regarding your research
interests, new journal articles, sequences and more from
PubMed and GenBank |
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Analysis |
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Bioconductor |
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Bioconductor.org
Homepage—Consortium of individuals that have created
an open source and code software package (Bioconductor)
designed to analyze genomic data using a bioinformatics
approach |
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National Center for Genome Research |
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NCGR
Homepage —The
National Center for Genome Resources (NCGR) in Santa Fe,
New Mexico, is an independent, nonprofit research institution
that develops and uses informatics for biological discovery |
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TIGR |
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The
Institute for Genomic Research—Provides access to
free research tools and software, databases, articles and
general news and information relating to genomics, microarrays,
and sequence analysis |
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BioASP |
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The BioASP Portal is the
bioinformatics service platform of Netherlands Bioinformatics Centre (NBIC). NBIC
provides access to databases and innovative applications (BioASP), supports cooperation
between researchers (BioRange) and coordinates education and training (BioWise). |
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Gene
Ontology/Annotation |
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Arrogant |
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Array
Organizing Tool (ARROGANT) from University of Texas
Southwest Medical Center—Software tool developed
to facilitate the identification, annotation and comparison
of large collections of genes or clones |
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BioCarta |
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BioCarta,
INc. Homepage—Company providing various biological
reagents as well as a well-curated and thorough pathways
database describing canonical pathways as well as new,
highly specific, or predicted pathways; pathways are presented
as highly detailed color images |
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DAVID |
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Database
for Annotation, Visualization, and Integrated Discovery
from NIAID/NIH—A web tool designed to take lists
of genes and group them based on their ontological annotations
in a visual manner; also provides pathway, annotations,
and domain tools |
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DRAGON
Database |
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Database
Referencing of Array Genes Online—Database providing
annotation information for genes as well as numerous tools
and links for microarray data analysis |
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EASE |
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Expression
Analysis Systematic Explorer from NIAID/NIH—A standalone
program designed to perform similar analyses to that of
DAVID but in a more robust fashion, employing statistical
anlysis and greater annotation information |
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Gene Ontology Consortium |
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Gene
Ontology Consortium Homepage-- The goal of the Gene Ontology
TM (GO) Consortium is to produce a controlled vocabulary
that can be applied to all organisms even as knowledge
of gene and protein roles in cells is accumulating and
changing. GO provides three structured networks of defined
terms to describe gene product attributes |
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GoMiner |
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GoMiner
from NCI/NIH—Tool for biological interpretation
of 'omic' data - including data from gene expression microarrays.
GoMiner classifies the genes into biologically coherent
categories and assesses these categories |
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MatchMiner |
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MatchMiner
from NCI/NIH—A set of tools that enables the user
to translate between disparate ids for the same gene |
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Onto-Express |
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Intelligent
Systems and Bioinformatics Laboratory at Wayne State University—A
web-based tool able to automatically translate lists of
differentially regulated genes into functional profiles
characterizing the impact of the condition studied |
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Resourcerer |
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RESOURCERER
from TIGR—Provides annotation based on the TIGR
Gene Indices (TGI) for commonly available microarray resources |
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Sequence |
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ATCC Bioproducts |
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ATCC
Molecular Bioproducts—Company
providing numerous biological reagents and supplies as
well as useful information on cell culture techniques,
cloing techniques and data, and links to related databases |
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BCM Search Launcher
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Baylor
College of Medicine Search Launcher—The
Baylor College of Medicine Search Launcher is an on-going
project to organize molecular biology-related search and
analysis services available on the WWW by function by
providing a single point-of-entry for related searches
(e.g., a single page for launching protein sequence searches
using standard parameters). |
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DNA Sequence
and Structural Analysis |
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DNA/RNA
Sequence Homology and Structural Analyses from the San
Diego Supercomputer Center—A wide array of sequence
analysis tools including Blast searches, ORF splice site,
and trans-factor/promoter binding predictions, sequence
alignments and restriction mapping along with many more |
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GENSCAN |
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GENSCAN
Web Server at MIT—This
server provides access to the program Genscan for predicting
the locations and exon-intron structures of genes in genomic
sequences from a variety of organisms |
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NEBcutter |
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NEBcutter
from New England BioLabs—This tool will take a DNA
sequence and find the large, non-overlapping open reading
frames using the E.coli genetic code and the sites for
all Type II restriction enzymes that cut the sequence
just once. By default, only enzymes available from NEB
are used, but other sets may be chosen |
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Primer3 |
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Primer3
Input from the Whitehead Institute/MIT Center for Genome
Research—A free web based primer design tool with
a high level of customizable parameters for primers |
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SDSC
Biology Workbench |
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Biology
Workbench at the San Diego Supercomputer Center at UCSD—The
Biology WorkBench is a web-based tool for biologists.
The WorkBench allows biologists to search many popular
protein and nucleic acid sequence databases. Database
searching is integrated with access to a wide variety
of analysis and modeling tools, all within a point and
click interface that eliminates file format compatibility
problems |
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Software |
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DNASTAR |
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DNASTAR
Homepage—Commercial company with many pieces of
software related to sequence analysis including primer
design, sequence assembly, protein structure predictions,
and alignments |
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Genomatix Suite |
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Genomatix
Inc. Homepage—Commercial software capable of searching
genomic sequence data for specific transcripts, loci,
and the like as well as performing analyses related
to promoters, transcription factor binding sites, and
general sequence analysis; provides demos and some free
access |
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MADIBA |
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MADIBA
Sequence Alignment Software from the University of Maryland
Biotechnology Center—A software package from the
alignment of nucleotide and protein sequences |
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pDRAW32 |
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pDRAW32
Homepage—Freeware software designed to do simple
sequence analysis but is also capable of storing annotation
information, primer, information, and vector design
information as well as perform restriction enzyme predictions
and simulate gel results |
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SEQtools |
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SEQtools
by Søren Rasmussen—SEQtools 8.2 is a comprehensive
win32 program package for handling and analysis of nucleotide
and protein sequences. The program includes a series
of trivial functions to help you carry out common operations.
In addition SEQtools will assist you with more demanding
tasks like unattended batch blast search at NCBI with
advanced facilities for retrieving, storing and listing
search results |
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Sequencher |
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Sequencher
DNA Analysis software from the Gene Codes Corp.—Commercial
software capable o f sequence alignments and assembly
as well as annotating sequences and performing RE and
ORF predictions |
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TIGR Analysis Software |
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Seqeuence
Analysis Software from TIGR—Numerous free software
programs designed for gene discovery, gene annotation,
gene prediction, gene alignment and various permutations |
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Vector NTI |
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Vector
NTI from Informax—Vector NTI Advance is the most
robust and highly integrated application available in
the market for desktop sequence analysis and molecular
biology data management |
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Microarray |
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Chip.org |
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Children’s
Hospital Informatics Program (affiliated with the Harvard
School of Medicine)—Contains lots of interesting
reading about the work of CHIP but also contains links
to software and other web resources for bioinformatics,
microarray, SNP, and clinical genomic research |
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Comparison
of Microarray Software |
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Personal
Website of Y.F. Leung—Compares various microarray
software applications including data management, image
acquisition, quantification, and analysis |
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DNA Microarrays |
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Personal
website (Dr. Leming Shi, National Center for Toxicological
Research/FDA) containing hundreds of links as well as
well as introductory information about microarrays, specifically
DNA microarrays, including relevant research publications,
corporate websites, and software and more |
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Eisen Lab |
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The
Lab of Dr. Michael Eisen at the Lawrence Berkeley National
Laboratory at the University of California, Berkeley—The
originators of free clustering software; provides free
access to clustering and microarray analysis software
as well as databases and web resources |
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MIAME |
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Minimal
Information About Microarray Experiments—Site containing
links and information regarding the information required
for the publication and adequate description of how microarray
data was generated and reported; includes checklists,
relevant publications, and a description/history of MIAME |
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Microarrays.org |
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A
public source for microarray protocols and software provided
by the DeRisi lab at the Univeristy of California, San
Francisco—A resource containing protocols and software
for microarray research, focusing primarily on cDNA/spotted/sutom
arrays |
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Public
Domain Software |
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Personal
Website of Wentian Li —List of microarray software
applications available for free |
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R
Package Software |
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Personal
Website ofKorbinian Strimmer—A comprehensive list
of microarray analysis software packages that use the
R programming language |
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Software |
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Acuity |
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Acuity
from Axon Instruments—A data storage and analsis
software suite that works alongside GenePix; normalization,
filtering, and clustering as well as some data management |
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Affymetrix |
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Affymetrix,
Inc. Homepage—Makers of the GeneChip oligonucleotide
microarray platform as well as Microarray Suite, GCOS,
and DMT analysis applications for the GeneChip platform |
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AMAD |
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AMAD
written by Dr. Joe DeRisi—Another Microarray Database:
Perl scripts for managing microarray data on flat files |
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ArrayDB |
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ArrayDB
from NHGRI/NIH—ArrayDB 2.0 is a software suite
that provides an interactive user interface for the
mining and analysis of microarray gene expression data.
All of the analyzed expression data from a microarray
experiment, as well as information about the clones
used in the experiment, are stored in a relational database |
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arraystats |
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arrraystats
written by Paul Pavlidis—Perl package of functions
and tools for manipulating microarray data and data
files, contains ANOVA and T-test functions |
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Array
Finder |
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Array
Finder tool from Affymetrix—A simple web-based
tool designed to find specific probe sets corresponding
to genes on the GeneChip microarray platform |
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ArrayViewer |
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ArrayViewer
from TIGR—A software tool designed to facilitate
the presentation and analysis of microarray expression
data, leading to the identification of genes that are
differentially expressed; written in Java |
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Array Pro |
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Array
Pro by Media Cybernetics—Array Pro Analyzer is
an indispensable tool for the nascent microarray and
high-throughput screening research efforts fueling the
genomics, proteomics, drug discovery and bioinformatics
revolution |
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Array
Vision |
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Array
Vision by Imaging Research—ArrayVision is a flexible
software package that has been developed for the quantification
of gene expression and protein arrays |
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BASE |
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BioArray
Software Environment from Theoretical Physics group
at Lunds University—BASE is a comprehensive free
web-based database solution for the massive amounts
of data generated by microarray analysis |
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Biodiscovery |
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Biodiscovery,
Inc.Homepage—Set of commercial software packages
designed to analyze and manage microarray data from
both cDNA and oligonucleotide microarrays |
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BRB Array
Tools |
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BRB
ArrayTools Homepage from the National Cancer Institute--BRB
ArrayTools is an integrated package for the visualization
and statistical analysis of DNA microarray gene expression
data; developed by statisticians experienced in the
analysis of microarray data and involved in the development
of improved methods for the design and analysis of microarray
based experiments |
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Centralizer |
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Centralizer
written by Alexander Zien—Centralizer is a program
that computes normalization factors for gene expression
data according to the centralization scheme |
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CIT |
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Cluster
Identifcation Tool written by Kyle Furge—Discrimant
cluster analysis of microarray gene expression data;
Requires interaction with Eisens' Cluster and TreeView |
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Clusfavor |
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CLUSter
and Factor Analysis with Varimax Orthogonal Rotation
written by Leif Peterson—CLUSFAVOR is a Windows-based
computer program for exploratory cluster and factor
analysis. CLUSFAVOR was designed for large sample problems
devoted to genomic analysis of gene expression data
from cDNA and oligonucleotide microarrays |
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Cluster |
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Cluster
written by Michael Eisen—Perform a variety of
types of cluster analysis and other types of processing
on large microarray datasets; Currently includes hierarchical
clustering, self-organizing maps (SOMs), k-means clustering,
principal component analysis; works in conjunction with
Treeview |
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CTWC Algorithm |
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Coupled
Two Way Clustering algorithm provided by the Weizmann
Institute of Science—Register for free access
to the CTWC algorithm and server to cluster expressional
data |
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Dapple |
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Dapple
written by Jeremy Buhler at the University of Washington—A
Program for Analyzing cDNA Microarrays. Dapple is a
tool for segmentation, spot-finding, and quantitation
of cDNA microarrays. It implements various algorithms
designed to make analysis of microarrays fast, accurate,
and convenient for the user |
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dCHIP |
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DNA-Chip
Analyzer from Harvard University—A free microarray
analysis software package that utilizes an intensity
modeling approach to microarray analysis |
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Expression Profiler |
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Expression
Profiler from J. VIlo at EBI—Expression Profiler
is a set of tools for clustering, analysis and visualization
of gene expression and other genomic data |
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F-Scan |
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F-Scan
from NIH—A free microarray analysis program from
NIH for analysis of fluorescently probed cDNA arrays |
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Freeview |
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Freeview
written by Marko Kavcic and Blaz Zupan—FreeView
and FreeOView are programs for viewing and optimizing
gene expression dendrograms |
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Gene Array Analyzer
Software |
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GAAS
created by MI Poli—GAAS is an integrated software
framework for efficient management, analysis and visualization
of large amounts of gene expression data across replicated
experiments. It is structured in management, analysis
and visualization sections that allow dealing with several
gene expression dataset formats, custom differential
expression data analyses, suitable visualization, and
storage of results |
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Geneclust |
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Geneclust
written by Paul Roebuck—GeneClust is a tool for
exploratory analysis of gene expression microarray data
featuring Hierarchical clustering and Gene shaving coupled
with simulation to assess performance of the above methods.
Needs S |
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GeneCluster
2 |
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Clustering
Software provided by the Whitehead Institute, Center
for Genome Research—Freeware clustering tool that
utilizes the weighted voting (WV) and k-nearest neighbor
(KNN) algorithms to cluster expression data |
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GeneDirector |
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GeneDirector
from BioDiscovery—GeneDirector helps you organize
and manage all data generated across the entire array
experimental process from array creation, sample preparation,
hybridization, image analysis to data analysis |
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GenePix Pro
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GenePix
Pro from Axon Instruments—GenePix Pro is a software
from Axon Instruments, Inc. for analyzing DNA and protein
micrarrays, tissue arrays and cell arrays; images acquired
from either Axon Scanner or third-party scanners can
be used |
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GeneSifter.net |
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VizX
Labs, Inc. Homepage—Commercial company and makers
of GeneSifter, a web-based microarray data analysis
software package, capable of comparison analyses from
any microarray data; includes statistical tests, functional
annotations, heat diagrams and scatter plots, and general
data analysis tools |
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Genesis |
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Genesis
from Graz University—A Java suite containing various
tools such as filters, normalization, visualization
tools, common clustering algorithms, SOM, k-means, PCA,
SVM, map gene onto chromosomal sequences |
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GeneSOM |
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GeneSOM
written by Jun Yan—R package for Clustering Genes
using Self-Organizing Map |
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GeneSpring |
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GeneSpring
from Silicon Genetics—GeneSpring is an all-inclusive
software program widely regarded as the gold standard
in expressional array analysis; includes clustering,
statistical analysis, data filtering, and database integration |
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GeNET |
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GeNet
from Silicon Genetics—GeNet is the most scalable
and robust expression data management solution available,
meeting the demands of both high-throughput sample volumes
and increasing numbers of users |
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GeneTraffic |
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GeneTraffic
from Iobion Informatics—GeneTraffic is offered
in three convenient packages: one for Affymetrix GeneChip
microarray data, one for standard two-color microarray
data, and one that is a combination package allowing
you to manage both types of formats |
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GeneX-Lite |
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GeneX-Lite
from NCGR—GeneX-Lite is a client application that
provides an interface to a relational database managment
system (RDBMS) |
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GESSES |
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GESSES
written by Joshua Deutsch—GESSES (genetic evolution
of sub-spaces of expressed sequences); The algorithm
computes an ensemble of predictors containing a minimal
number of genes |
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gp3 |
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GenePix
Post-Processing Script from the Zacharewski Lab at Michigan
State University—A Perl script that takes a GenePix
results file and processes the raw data from it by performing
signal filtering, background correction and signal normalization |
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ISIS |
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ISIS
written by Anja von Heydebreck and Wolfgang Huber—ISIS
is an R/C++ implementation of the class discovery method
for gene expression data |
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J-Express
Pro |
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J-Express
Pro from Molmine—J-Express Pro is a comprehensive
portable software package for analysis and visualisation
of microarray data. The program gives access to multidimensional
scaling, clustering, and visualisation in an integrated
and flexible way. Its efficiency allows interactive
clustering of thousands of expression profiles on standard
personal computers |
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KNNimpute |
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KNNimpute
distrubuted through Stanford University—KNNimputeis
a program for estimating missing values for gene expression
data |
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Maanova |
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Maanova
from the Jackson Laboratory—MicroArray ANalysis
Of VAriance (maanova) provides a complete work flow
for microarray data analysis including: Data quality
checks and visualization, data transformation, ANOVA
model fitting for both fixed and mixed effects models,
statistical tests including permutation, confidence
interval with bootstrapping, cluster analysis; R add-on
package |
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Matrix2PNG |
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Matrix2PNG
written by Paul Pavlidis—Converts a gene expression
matrix to an image in .png format |
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MaxD |
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MaxD
from Manchester University—Maxd is a data warehouse
and visualisation environment for genomic expression
data |
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Microarray Explorer |
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Microarray
Explorer (MAExplorer) software from the Laboratory of
Experimental and Computational Biology at the National
Cancer Institute— A free software package designed
to analyze gene expression data from cDNA or oligonucleotide
microarrays |
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MicroArray
Suite |
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MicroArray
Suite from Scanalytics—MicroArray Suite is Scanalytics
image analysis software for visualizing and extracting
data from DNA microarrays |
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NetAFFX |
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NetAFFX
Analysis Center from Affmymetrix—A collection
of analysis tools and database information related to
the analysis of GeneChip data; includes annotations,
NCBI links, sequence information, and a functional ontology
tool(requires free registration) |
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NOMAD |
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Nomad
from UCSF—NOMAD is an open source system for storing
and querying the results of microarray experiments |
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PAGE |
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Patterns
from Gene Expression from the University of Pennsylvania—PaGE
is a tool to attach descriptive yet dependable, and
easily interpretable expression patterns to genes represented
in a collection of hybridization array experiments (macro-
or micro-arrays); In particular, this incorporates a
novel method to identify differentially expressed genes
between two sample types with attached measures of confidence
in the predictions made |
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PAM |
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Prediction
Analysis for Microarrays from Stanford University—PAM
does sample classification via nearest shrunken centroids,
with many features including built-in cross-validation |
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Pickgene |
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Pickgene
written by Brian Yandell—Functions to Analyze
Microarray (Gene Expression) Data; currently available
through BioConductor |
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QT_Clust |
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QT_Clust
written by Witold Wolski—This is a reimplemantation
of the QT_clust algorithm |
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Rosetta
Resolver |
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Rosetta
Resolver from Rosetta Biosoftware—The Rosetta
Resolver system is a versatile and robust enterprise,
gene expression data analysis system; also includes
data management features |
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SAM |
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Significane
of ANalysis of Microarrayswritten by R. Tibshirani—Supervised
learning software for genomic expression data mining |
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ScanAlyze |
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cDNA array quantitation software written by Michael
Eisen —Software for quatification of array signals
from fluorescently labeled cDNA arrays |
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SMA |
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Statistical Microarray Analysis from UC, Berkeley—The
package contains some simple functions for exploratory
microarray analysis |
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Spot |
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Spot written by Jean Yang and Michael Buckley—Software
for analysis of microarray images, built on top of Richard
Beare's image analysis package, "Voir" |
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Spotfire |
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Spotfire, Inc. Hompage—Commercial software for
data management and analysis of microarray data and
functional genomic information |
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SVDMAN |
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SVDMAN written by Michael Wall and Patricia Dyck—Singular
Value Decomposition Microarray Analysis is a program
for singular value decomposition analysis of global
gene expression data |
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TM4 |
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TM4 Microarray Analaysis Packagee—A suite of microarray
analysis software used primarily for cDNA micrarray
analysis; includes software for spotfinding, quantification,
and annotation |
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tpWY |
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tpWY from the University of Pennsylvania—This
program computes t-statistics and p-values (both unadjusted
and adjusted according to the Westfall and Young step-down
algorithm) for two-sided alternative hypotheses |
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Treeview |
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Treeview written by Michael Eisen—Graphically
browse results of clustering and other analyses from
Cluster; Supports tree-based and image based browsing
of hierarchical trees; works in conjunction with Cluster |
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Vector Expression |
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Vector Expression from Informax—Micrarray analysis
suite using a friendly graphical interface and containing
a complete set of peer-reviewed gene expression analysis
tools |
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VERA
and SAM |
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VERA and SAM maintained by Institute for Systems Biology
and the WHitehead Institute—VERA - Variability
and ERror Assessment: Estimates error model parameters
from replicated, preprocessed experiments. SAM - Significance
of Array Measurement: Uses error model to improve the
accuracy of the expression ratio and to assign a value
'lambda' to each gene, indicating the likelihood that
the | | |