updated 05-Feb-2007
Genomics: Databases
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UCSC Genome Browser
NCBI GenBank
EMBL-EBI Integr8 Genome Browser
Galaxy: comparison of genomic datasets
GNF Symatlas (expression for >30,000 Hs & Mm targets)
Signal Transduction Knowledge Environment
Reactome – a knowledgebase of biological pathways
Pharmacogenomics Knowledge Base
AfCS-Nature Signaling Gateway
NCBI Genome Projects
NHGRI Genome Hub
NCBI home
Sanger Center
EMBL European Bioinformatics Institute
EMBL Nucleotide Sequence Database
Ensembl Genome Browser
Ensembl Multi-MartView
NCBI Map Viewer
NCBI UniGene
NCBI whole genomes
UCSC Genome Bioinformatics
UCSC Table Browser
Connectivity Map expression+bioactive small molecules
Eukaryotic Promoter Database
DNA Data Bank of Japan
TIGR Gene Indices
Gene Ontology
InterPro Protein Annotation Database
TRANSFAC transcription factor DB
Database of Interacting Proteins
Kyoto Encyclopedia of Genes and Genomes
Negative Proteome Database
GNF Gene Expression Atlas (old)
Computational Biochemistry
Computational Biochemistry
Cytochrome P450 Homepage
EcoCyc
DNA tools
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Entrez-DNA
Batch Entrez
BCM Sequence Tools
DNA/RNA database list
Biology Workbench (reg req)
DeCypher
BDGP Sequence Analysis Tools
Codon Usage Tables
BCM genefinder
Gene Finder List
GeneMachine- Gene Finding & Annotation
GeneScan server at MIT (reg req)
Genie gene finder
Promoter Prediction
RepeatMasker at BCM
RepeatMasker at EMBL
Web Primer
OligoAnalyzer - IDT
Ensembl Trace Server
Random DNA Sequence Generator (more options)
Random DNA Sequence Generator
UCSC In-Silico PCR (useful for QPCR primer design)
Genomics: Tools/Software
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BioWareDB: search engine for bioinformatics software
List of Proteonomics Tools
BCM Search Launcher
Biology Workbench (reg req)
SDSC biotools
DNA/RNA database list
Molecular Information Agent
EMBOSS for Windows (Command Line)
Staden Package (EMBOSS GUI)
Molecular Biology Freeware for Windows
Metagraph Database Open Source
MB: free Windows DNA analysis program
SEQtools: free win32 software suite for nuc & prot seq
Affymetrix NetAffx
DeCypher Search
Gene Finders List
GenoMiner: ID of conserved sequence tags
Gepasi3 Biochemical Kinetics Sim
SDSC: Bioinformatics & Computational Bio
LUMIER: Luminescence-based Mammalian Interactome
SMART Protein Search
The Virtual Cell
E-Cell Project
RNA tools
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RNAdb: ncRNA database
Rfam: noncoding RNA database
Noncoding RNA Database
A portal site for functional RNAs and noncoding RNAs
Functional RNA Database
UCSC Genome Browser with ncRNA custom tracks
IMB RNA World Website
DNA/RNA database list
miRBase: microRNA database
ASRP: Arabidopsis thaliana small RNA project
snoRNAbase: human H/ACA and C/D box snoRNA
Map of Structural RNAs in the Human Genome
MicroRNA and putative targets
Plant ncRNAs
RNAshapes: RNA structure analysis
CMfinder: RNA motif finding
GNF Expression Data
Literature Searches
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Entrez PubMed
Google Scholar
OMIM (Human Disease Genetics)
Online Biology Textbooks (NCBI)
Batch Entrez
Google U.S. Patents searching
BioInfoBank Library (PubMed searches with citations)
IUPAC List of Chemical Terminology
Melvyl- Medline+CA Digital Library
Molecular Information Agent
NIH Grants Database
Digital Library of Theses and Dissertations
Statistics Tutorial
Electronic Journals (UCSD only)
Scripps E-Journals (TSRI only)
UCSD Biomed Library
Google Newsgroups Search
Google Images Search
Google Labs (Google's Technology Playground)
CIA World Factbook
Bartlett's Familiar Quotations
Protein tools
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Entrez-protein
InterPro Domain Searching
Pfam HMM functional domain searching
SMART: domain and homology searching
Biology Workbench (reg req)
BCM: General Protein Sequence Analysis
Similarity Search Engines
BCM: Protein Secondary Structure
BCM:Multiple Sequence Alignments
Clustalw and Dendrograms
Batch Entrez
DeCypher Search
DAS-TMfilter server
HMMtop Transmembrane Prediction
TMAP transmembrane prediction
SDSC family pairwise search
MEME/MAST motif discovery
InterPro: protein function and domains
Database of Interacting Proteins
BIND: Biomolecular Interaction Network Database
BLOCKS-PRINTS server
Swiss Protein Knowledgebase
Human Genome
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UCSC Browser: Human
Ensembl Human Genome Central
ENCODE project at UCSC
H-InvDB: Human gene database
OMIM (Human Disease Genetics)
SNP Consortium
Ensembl SNP viewer
International HapMap Project browser
South African STACK Project
CAGE Analysis Viewer (human)
BLAST
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NCBI BLAST home
Sanger Center: BLAST
BLAST 2 sequences (alignments)
Do It Yourself BLAST web interface
BLAST the TIGR Gene Indices
NCBI CD-search
BLASTN
BLASTP
BLASTX
TBLASTN
TBLASTX
PSI & PHI BLAST
Human Genome Blast Server
RIKEN mouse cDNA BLAST
BDGP - Drosophila BLAST
Sanger Center: Worm BLAST
Raw Seq Trace BLAST
Model Systems: Mouse
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UCSC Browser: Mouse
Mouse Genome Informatics
Genelynx: a portal to the mouse genome
FANTOM 3 (functional annotation of mouse)
FANTOM 3 Database
FANTOM 2
SADB: Sense and Antisense DataBase
CAGE Analysis Viewer (mouse)
Ensembl Mouse Genome Server
Mouse Gene Imprinting Map
UCSC Blat Search Mouse Genome
Sanger Institute Mouse Blast Server
Ensembl Mouse Blast
Rat Genome Database
RNA Interference (RNAi)
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Tuschl lab siRNA user guide
siRNA design – metasearch using existing software
IDT siRNA design tool
Ambion's siRNA target finder and design tool
BIOPREDsi siRNA design - Novartis
DEQOR siRNA design tool
Dharmacon siRNA picker
EMBOSS siRNA design tool (web-GUI)
Genescript shRNA builder
Genescript siRNA design tool
Invitrogen siRNA design tool
Jack Lin's siRNA sequence finder
Qiagen siRNA design tool
Smith Waterman Analysis (single seq)
Sfold siRNA design – Wadsworth Bioinformatics Center
SiDE siRNA design – CIPF Spain
siRNA design – Whitehead (login req)
siSearch siRNA design – Stockholm Bioinformatics
U of Tokyo siRNA design tool
Wistar Institute siRNA design tool (Dharmacon rules)
Model Systems: Drosophila
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Flybase: Genetics, Genes, Functions, Etc
Flybase Batch Download
UCSC Browser: Fly
UCSC Blat Search Fly Genome
BDGP-fly specific BLAST
BDGP-Flybase megasearch
Berkeley Drosophila Genome Project
Fly Enhancer: search for DNA binding sites
HOMOPHILA- human+fly disease genes
Gadfly Batch Download
Gadfly: molecular info in genes
Database of insect P450 family
Electron micrographs of chromosomes
Protocols
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Current Protocols Online
Protocols Online - searchable database
BD Fluorescence Spectrum Viewer Java 2
Omega Curv-o-matic
The Axon Guide: electrophysiology
Yeast 2-Hybrid Screening
NIH image
Brown Lab Home-built Microarray
Model Systems: C. elegans
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WormBase (C. elegans)
AceDB (Caenorhabditis elegans)
UCSC Browser: Worm
Microarrays
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Affymetrix Transcriptome Project
GNF SymAtlas (Gene Expression profiles)
Affymetrix NetAFFX
Affymetrix Tiling Array Tools
Affymetrix Integrated Genome Browser (IGB)
Microarray Libraries (Insightful.com)
Partek Genomics Suite Software
Spotfire DecisionSite
GNF Gene Expression Atlas (old)
Model Systems: Other
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Arabidopsis Genome Initiative
Arabidopsis Information Resource
Comprehensive Yeast Genome Database
Saccharomyces Genome Database
Yeast Protein-Protein Complexes
Schizosaccharomyces pombe Genome Project
TIGR Comprehensive Microbial Resource
TIGR Microbial Database
EcoGene (Escherichia coli)
Zebrafish Information Network
Jobs
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Nature's Career Site
Science Magazine's Career Site
List of Bioinformatics Companies
Job Lists: BioSpace.com
Job Lists: craigslist- Bay Area
Job Lists: Monster.com
Job Lists: The Scientist
Job Lists: BayArea Jobs.com