Useful Molecular Biology Bookmarks
Provided by Sidney Morris, Ph.D.
"This is a collection of databases and Web-based utilities that I have found useful for research and teaching purposes. Distinct from most such collections is the BASIC TOOLKIT section, which lists programs and Web sites that should meet the most common needs of many users. In some sections I have listed multiple sites for some types of analyses because not all Web utilities provide exactly the same functionality and flexibility of application. Based on my own interests, this collection is biased toward analysis of vertebrate sequences but links to other species can be tracked down from the resources listed here. This collection is by no means comprehensive, so if you can't find what you are looking for here, check the mega-collections of links under Section III. "
I. GETTING STARTED: TUTORIALS AND GUIDES
- BLAST tutorials
- Tutorial: Finding homologs with BLAST
- Primer on Finding Homologous Proteins or Genes
- Tutorials Available at NCBI
- Tutorials for NDB Structure Finder
- NCBI Coffee Break: Contents
- (SRS User's Manual)
- Iterated profile searches with PSI-BLAST
- BioScience Forum - Discuss Molecular Biology and Bioinformatics
- EBI: Bioinformatics Educational Resource: Databases
- EBI: Bioinformatics Tutorials
- EBI: List of Bioinformatics Educational Resources
II. BASIC TOOLKIT
A. RECOMMENDED FREE SOFTWARE
- BioEdit Sequence Alignment Editor for Windows 95/98/NT
- About Chime and Where to get it
- GeneDoc HomePage
- Download ClustalX
- Protein Explorer FrontDoor
- EnzymeX - Restriction site analysis (Mac only)
- Chimera: Interactive Molecular Visualization
B. WEB-BASED TOOLS
- NCBI Site Map: Guide to NCBI Resources
- Entrez cross-database search
- BLAST at NCBI
- Advanced BLAST at EMBNET
- EBI Tools: Blast, Fasta, Sequence Analysis, Homology Searches, Sequence Translation, Protein Annotation, Genomes, Proteomes, Sequence Alignments
- The Sequence Manipulation Suite
- Webcutter 2.0 - Restriction Analysis
- NEBcutter V2.0
- READSEQ: Convert a Sequence to Different File Formats
- SDSC Biology Workbench
- Translate DNA to Protein--ExPASy
- ExPASy - Tools
- Protein Sequence Alignments at BCM
- CUTTER: A tool to generate and analyze proteolytic fragments
- PubCrawler: An update alert service
- RefScoutŪ - Keeps track of your references
- HighWire--Journal text search and email alert
- BioMail: Automate custom PubMed searches
- Human Genome Working Draft
- The I.M.A.G.E. Collection of Vertebrate Genes
- Mammalian Gene Collection
- PubMed Bookshelf resources
- BioQuery: Integrated Interface to BioMedical Databases.
III. MULTI-LINK LISTS OF DATABASES AND ANALYTICAL TOOLS
- #1--The CMS-SDSC Molecular Biology Resource
- #2--ExPASy Molecular Biology Server
- #3-BCM Search Launcher Page
- #4--Amos' WWW links page
- #5--Mol Biol Database Collection--NAR 2003
- Mol Biol Tools at Nucl. Acids. Res. (31 [13]) 2003
- NAR Database Issue
- HSLS: Molecular Biology & Genetics
- Bioinformatics Supercomputer Utilities
- LabVelocity : Tools
- 123 Genomics: genomics and bioinformatics resources
- http://www.bioinformatics.vg/index.shtml
- ABIM Online analysis tools
- http://www.gene-regulation.com/pub/programs.html#matinspector
- The Catalog of Databases
- Research Tools
- GenomeNet WWW server
- Harvard Dept of MCB - Biology Links
- All the Virology on the WWW
- Virtual Library: Biosciences
- Links to the Genetic World: 1
- Swiss EMBnet node server
- BioInfo Bank
- Biomolecules Gallery
IV. SEARCH DATABASES
- BLAST at NCBI
- Advanced BLAST at EMBNET
- Entrez Browser
- BLAST Human Ensembl Genome Server
- BLAST the Human Genome
- NCBI Reference Sequence (RefSeq)
- GOLD: Genomes OnLine Database Homepage
- SWBIC - BLAST Filter
- BLAST Mouse Ensembl Genome Server
- BLAST Drosophila Ensembl Genome Server
- SRS (Sequence Retrieval System) v6 Multi-database search/analyses
- (SRS User's Manual)
- The EMBL Nucleotide Sequence Database
- GeneNest: gene indices as clusters of ESTs
- MutationDiscovery.com
- euGenes: Model Eukaryotic Organism Genes
- PubGene
- ORNL GenQuest Form
- SDSC Biology Workbench
- Search IMAGE Database of Human Genes
- SWISS-PROT and TrEMBL
- NCBI Taxonomy Browser
- Animal Genome Size Database
- EBI Databases
- Bio Netbook
- Human BLAT Search
- WiGID - Wireless Genome Information Database
- The Sanger Institute : Data Search
V. DATABASES
A. EST DATABASES
- EBI's EST Links
- dbEST NCBI (cDNA database)
- The I.M.A.G.E. Collection of Vertebrate Genes
- TIGR Gene Indices - The Institute for Genomic Research
- Mammalian Gene Collection
- stackPACK v2.2: cluster, align, analyze ESTs
B. HUMAN DATABASES
- Ensembl Human Genome Server
- BLAST the Human Genome
- BODY MAP--human & mouse gene expression database
- GeneCards: human genes, proteins and diseases (Weizmann)
- Genome Catalog - human
- GRLviewer: Human Gene Resource Locator
- BCM Human Transcript Database Home Page
- Human Genome Sequencing--BLAST and Progress Reports
- The Genome Database
- Human Genome Browser Gateway
- HUNT: Human Full Length cDNA Database
- LocusLink: An Integrated Information Site for Human Genes
- NCBI Human Genome Guide: External Links
- OMIM Home Page -- Online Mendelian Inheritance in Man
- TIGR Human Gene Index
- UniGene-Human
- UTR Extender for Human mRNAs
- HGVbase - Human Genome Variation database
- Genelynx: A portal to the human genome
C. MOUSE DATABASES
- BODY MAP--human & mouse gene expression database
- Ensembl Mouse Genome Server
- Genome Catalog - mouse
- Mouse Genome Browser Gateway
- Mouse Genome Home Page--JAX
- Mouse Genome Index v2.3 -Gene Expression Menu
- Edinburgh Mouse Atlas Project Database
- TIGR MOUSE Gene Index
- RIKEN Mouse Encyclopedia Index
- Unigene- Mouse
- The Whole Mouse Catalog
C.1. TRANSGENICS AND KNOCKOUTS
TBASE-Mouse Knockouts
- Cre transgenic database - published lines
- List of Floxed Genes
- Mouse knockouts--Skarnes Lab Gene Traps
- http://mouseblast.informatics.jax.org/
- Blast The Mouse Genome
- Genelynx: A portal to the mouse genome
D. RAT DATABASES
- RATMAP: The Rat Genome Database
- TIGR Rat Gene Index
- Unigene-Rat
- BLAST Against Baylor Rat Sequences
E. YEAST DATABASES
- Saccharomyces Genome Database
- Webminer: Gene expression in yeast
- Yeast Genome Deletion Project
- Yeast Genome Catalog
F. OTHER SPECIES DATABASES
- List of Genomes at NCBI
- ARK Multiple Species Databases
- WormBase (C. elegans)
- C. elegans Gene Index at TIGR
- Drosophila Gene Index at TIGR
- FlyBase Drosophila Genome
- Genome Channel
- Mullti-species Gene Indices at TIGR
- Zebrafish Blast Server
- ARKdb-pig Public Database Browser
- Parasite Consensus EST Databases
- Retroviruses
- Virtual Genetics Library for Plants, Animals, Bacteria
- Genome Tools for Microbes
- Ciona Genome Project
- OMIA: Online Mendelian Inheritance in Animals
- The Viral Reference Genomes
- Microbiology Microbes Bacteria Information and Links
- BLAST Against Baylor Bovine Sequences
- BLAST Against Baylor Chimpanzee Sequences
- Search for ORFs in bacterial genomes
G. VECTOR DATABASES
- Screen DNA Sequence for Vector Sequences with VecScreen
- VecScreen Database of Vectors
- I.M.A.G.E. Consortium Vectors
- Maps of common vectors
- Redasoft ResearchNet - Cloning Vector Search Engine
H. MORE DATABASES - UNSORTED
- Databases available at SRS
- COG
- Complete Genome Tracking Database
- The I.M.A.G.E. Collection of Vertebrate Genes
- Alliance for Cellular Signaling (AfCS)
- KEGG Regulatory Pathways
- OWL Protein Sequence Database
- Phosphoprotein Database (PPDB)
- Protein Data Bank (PDB) at RCSB
- SAGE (Serial Analysis of Gene Expression)
- SPAD : Signaling PAthway Database
- Transfac databases (not free)
- TreeBASE /Phylogeny Home Page
- The WWW Virtual Library: Model Organisms
- Proteome Analysis Database
- Official REBASE Homepage
- Protein-DNA Recognition Database
VI. DNA ANALYSIS TOOLS
A. BASICS: SEQUENCE ASSEMBLY AND EDITING; FORMAT CONVERSION
- BCM Search Launcher: Sequence Utilities
- READSEQ: Convert a Sequence to Different File Formats
- Sequence: complement, reverse complement, reverse
- CAP3 Sequence Assembly Program
- CAP : Sequence Assembly Program
- BLAST output to FASTA format
- CloneIt Online - Simulated Cloning Utility
- Screen DNA Sequence for Vector Sequences with VecScreen
- RepeatMasker--Screen for repeats and low complexity DNA sequences
- TAP - Transcript Assembly Program (EST-based)
- Submit a Sequence to GenBank
- pDRAW32 - DNA cloning, sequence analysis and plasmid/DNA plotting
- Savvy (draw plasmid map in SVG format)
B. RESTRICTION ANALYSIS
- Restriction Enzyme Site Mapper version 3
- Webcutter 2.0 - Restriction Analysis
- NEBcutter V2.0
- WatCut: Digest your DNA online, and create new restriction sites with silent mutations
- EnzymeX - Restriction site analysis (Mac only)
- Official REBASE Homepage
- In silico restriction digest of complete genomes
C. ALIGNMENTS
- Pairwise Alignment of DNAs: Blast 2
- Pairwise DNA Alignment Tool
- SIM4 - cDNA and Genomic DNA Alignment
- Multiple Sequence comparison tools
- Gene2EST: BLAST and align genomic DNA with ESTs
- BLAT: Search/Alignment Tool for Human Genome
- CONSENSUS sequences in unaligned DNA and protein sequences
- PipMaker and MultiPipMaker
- QAlign (download)
- SWBIC GraphAlign
- Spidey -- mRNA to genomic alignment at NCBI
- Wise2: Dna Block Aligner
- VISTA Alignment Tools for Comparative Genomics
- Alfresco: Comparative genome visualization tool
- DOTLET: Dot matrix alignment
- Dot matrix plot
- CodonAlign
- Pairwise alignment utililty
- Clustalw: Multiple alignments
- MAVID, for multiple genome alignments
- The Gibbs Motif Sampler for DNA
D. VISUALIZE ALIGNMENTS
- BOXSHADE 3.33 Alignment Viewer/Printer
- CINEMA 2.1 sequence alignment editor
- CINEMA 5 sequence alignment editor
- MVIEW multiple alignment viewer
- Drawseq - biosequence drawing tool
- Vista Genome Browser
E. TRANSCRIPTION FACTOR SITES
- Alibaba2 (uses Transfac 4.0)
- SiteSeer (uses Transfac 6.0)
- MatInspector V2.2 (uses Transfac 4.0)
- PatSearch 1.1 for TF sites
- PromoSer: The mammalian promoter service
- PROSPECT: Yeast Promoter Inspection Tool
- SIGSCAN: Transcription Factor DNA Scan (uses Transfac 2.5)
- TESS: Scan for Transcription Factor Sites (uses Transfac 4.0)
- TFSEARCH (uses Transfac 3.3)
- DBTSS: Database of transcription start sites
- Transcription Factor Site Scan
- Classification of Transcription Factors (1999)
- TRANSFAC - The Transcription Factor Database
- Transcription Regulatory Regions Database (TRRD)
- TRANSCompel--Composite Regulatory Sites
- Gene Regulatory Sequence Analysis
- PRESTA promoter database (PRomoter-EST association)
- Eukaryotic Promoter Database
- RSAT: Regulatory Sequence Analysis Tools
- MATCH tools for transcription factor sites (uses Transfac 3.5)
- Target Explorer
- Protein-DNA Recognition Database
- Genomatix: Gene2Promoter
- ConsInspector: transcription factor binding site prediction (download)
- FastM and ModelInspector (use Transfac 4.0)
- CONSITE
- DNA sequence utilities at Softberry
F. TRANSLATE DNA TO PROTEIN; CODON USAGE
- Translate DNA to Protein--ExPASy
- ORF Finder
- GeneMark 2.4: Analyze DNA sequence
- Transeq: Translate DNA to protein
- DNA Sequence Translator
- Codon Usage Database for Different Species
- Backtranslate Protein to DNA
- Reverse Translate a Protein
- Create codon usage table from DNA sequence
- Codon usage table analysis
- Countcodon program
- JavaScript DNA Translator 1.1
G. DNA ANALYSIS TOOLS - UNSORTED
- Link list: Tools for sequence comparisons
- Sequence Analysis wwwTools
- fastDNAml (DNA phylogenetic trees)
- Gene Identification
- Genome Channel
- Analyze Unknown DNA Sequence with NIX
- NetGene2: Predict splice sites
- spliceNest: Visualize splicing of genes from EST data
- UTR Extender for Human mRNAs
- PatSearch
- Kangaroo pattern search
- MEME: Discover motifs
- stackPACK v2.2: cluster, align, analyze ESTs
VII. RNA : GENE EXPRESSION AND SEQUENCE ANALYSIS
A. GENE EXPRESSION
- Gene Expression Omnibus Home
- SAGE Genie
- SAGEmap at NCBI
- x Profiler at CGAP: Tissue Expression Profiles
- DigiNorthern1: Virtual Northern of EST expression
- DigiNorthern 2: Compare expression of 2 ESTs
- GETMaps: Tissue-specific Transcript Mapping
- 123 Genomics - Gene Expression, Microarrays, DNA chips and Differential Displays
- GeneHopper - Main page
B. ANALYZE SECONDARY STRUCTURE AND UTRs
- Algorithms, thermodynamics and databases for RNA secondary structure.
- paRNAss: Predict RNA Secondary Structure
- Sfold - Software for Statistical Folding and Rational Design of Nucleic Acids
- Folding utilities at Zuker Lab
- Vienna RNA Secondary Structure Package
- The RNA World Website
- The RNA WebRing
- Rnadraw Homepage
- UTR Homepage
- ProSplicer: splicing database
- RnaViz: Visualize RNA Structure
- RNAML: tools to exchange RNA info
- Gutell Lab Comparative RNA Web Site
C. siRNA
- siRNA Converter
- siRNA Target Finder
- siRNA Construct Builder
- Imgenex : siRna tool
- siRNA Designer
VIII. DNA PRIMERS
- Primer3 Input (primer3_www.cgi v 0.2)
- Web Primer: PCR and Sequencing
- PDA -Primer Design Assistant
- The Primer Generator
- CODEHOP: design of degenerate primers
- PCR Guide
- GeneFisher - Interactive PCR Primer Design
- NetPrimer: Primer analysis at Premier Biosoft
- DoPrimer
- Primer Selection (Text)
- Oligo Calculator
- Molecular Probe Data Base
- ExonPrimer - Primer Design
- PROBEmer: Primer design for target families
- PrimerX
- In silico experiments with complete bacterial genomes: PCR, AFLP-PCR, PFGE
IX. PROTEINS: ANALYSIS TOOLS AND DATABASES
A. DATABASES WITH SEARCH AND ANALYSIS TOOLS
- Protein Data Bank (PDB) at RCSB
- Protein Information Resource Home Page
- Human Protein Reference Database
- BRENDA - Enzyme Database
- Search EC Enzyme Database
- InterPro Protein Database
- GeneQuiz - Homolog search
- ParAlign and SWMMX
- Pfam : Home page (St. Louis)
- COG: Clusters of Orthologous Groups of proteins
- DIP: Database of Interacting Proteins
- OWL Protein Sequence Database
- PALI: Phylogeny and ALIgnment of Homologous Protein Structures
- Kinase Sequence Database Version 3.0
- LigBase: database of aligned ligand binding sites
- Molecule Pages - AfCS Gateway
- Phosphoprotein Database (PPDB)
- The ProDom protein domain database
- PEDANT Protein Analysis Tools
- Proteome Analysis in Multiple Species
- Protein-Nucleic Acid Recognition Database
- Protein Kinase Resource
- ProtoMap: Classification of Proteins at SWISSPROT
- SAWTED Server: Search for homologs
- JAKs and STATs
- Alerts of New Sequences at SWISS-PROT
- Proteome
- SBASE - a protein domain library
- Pattern Search in Protein Databases
- The Protein Mutant Resource
- Human Mitochondrial Protein Database
- Advanced BLAST at EMBNET
- Receptome
- BCM Search Launcher: General Protein Sequence/Pattern Searches
B. SEQUENCE ALIGNMENTS
- Protein Sequence Alignments at BCM
- SIM Alignment Tool - Protein Sequences
- ClustalW Alignment with Dendrogram (at DeCypher)
- Clustalw
- ClustalX (download)
- T-COFFEE Multi-sequence alignment
- DCA: Divide-and-Conquer Multiple Sequence Alignment
- ConSurf: Map Degrees of Sequence Conservation in Aligned Proteins
- STRAP: refinement of huge multiple alignments
- CONSENSUS sequences in unaligned DNA and protein sequences
- POA -- Sequence Alignment
- Multiple Sequence Analysis Menu
- MEME - Introduction
- DOTLET
- SWBIC GraphAlign
- PRALINE: iterative multiple alignment using secondary structure
- Protein Hub
- HOMSTRAD
- HOMSTRAD/PLUS
- FUGUE: sequence-structure homology recognition and alignment engine
- JOY
- ALIGN
- Alignment App
- Wise 2: Align protein w/ genomic DNA
- The Gibbs Motif Sampler for Proteins
- EMBL Blast Protein Sequence Retrieval Tool - Input Form
- PipeAlign: new session
- PeCoP: Search for Conserved Positions/Residues
C. VISUALIZE PROTEIN ALIGNMENTS
- GeneDoc HomePage
- BOXSHADE 3.33 Alignment Viewer/Printer
- CINEMA: Interactive Multi-alignment Editor
- Easy execution of ESPript 2.0 / ENDscript 1.0
- MVIEW multiple alignment viewer
- ModView
- ConSurf: Map Degrees of Sequence Conservation in Aligned Proteins
D. STRUCTURE PREDICTION AND ANALYSIS
- A Guide to Structure Prediction
- ExPASy - Tools
- PSIPRED: a protein structure prediction server
- http://pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_server.html
- BioCoRE: A Tool-Oriented Collaboratory for Structural Biology
- ESyPred3D: Predict protein 3D structure
- BCM Search Launcher: Protein Secondary Structure Prediction
- 3D-JIGSAW Protein Comparative Modelling Server
- http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSAHLP/npsahlp_locsoft.html
- Protein Secondary Structure Prediction at BCM
- Prediction servers for DNA and Protein Sequences
- Sequence Analysis wwwTools
- Emotif: exploring the motif universe
- PeptIdent: Identify proteins
- Pfam : Home page (St. Louis)
- STING - Sequence To and withIN Graphics
- CDART: Conserved Domain Architecture Retrieval Tool
- FUGUE: Align sequences against structures
- FUGUE Profile Lib Search
- GeneFIND Protein Family Identification System
- GENO3D : AUTOMATIC MODELING OF PROTEINS THREE-DIMENSIONAL STRUCTURE
- GRASS Browser: Graphical Representation and Analysis of Structure Server
- HMMTOP transmembrane/topology prediction
- HOMSTRAD: Homologous Structure Alignment Database
- MOTIF: Searching Protein and Nucleic Acid Sequence Motifs
- Multilink List for Protein Sequence Analysis
- NNPREDICT
- Predict mitochondrial targeting sequence with MITOP
- Predicting Protein 3D structure
- Compare and align 3D protein structures
- PROSPECT (Protein Structure Prediction)
- Protein Fold Prediction
- PSORT WWW Server
- SBASE Protein Domain Library
- SignalP: Predicts Signal Peptides
- SubLoc 1.0: Predict subcellular location
- SWISS-MODEL Protein Modelling Server
- TMHMM 2.0---transmembrane prediction
- TMAP: Transmembrane Sequence Predictor
- TraDES: A New Way to Explore Protein Conformational Space
- Comparative Sequence Analysis by SMART (Simple Modular Architecture Research Tool)
- Trees from Blocks
- Mathematical Biology at the National Institute for Medical Research - NIMR
- SBASE structure prediction
- NCBI VAST Home Page
- Home page of ANTHEPROT
- ProtFun 2.1 Server
E. VISUALIZE PROTEIN STRUCTURE
- Find and visualize structures at The Protein Data Bank
- Protein Explorer FrontDoor
- DeepView - Swiss PDB Viewer Home Page
- Chimera: Interactive Molecular Visualization
- Cn3D Home Page
- Annotated list of modeling programs
- BioEditor Structure Annotation Tool
- List of FREE Modeling Software
- Free Molecular Visualization Software
- MOLMOL - MOLecule analysis and MOLecule display
- Molpov 2
- NIH "Molecules R Us" Structure Viewer
- RasMol Home Page
- Visual Molecular Dynamics--3D Graphics
- World Index of Molecular Visualization Resources
- Collaborative Molecular Visualization in ToolSpace
- Database of Macromolecular Movements
- Chime Square
- WebMol by Dirk Walther (UCSF)
- PDB to MultiGif Page
- VRML File Creator for Chemical Structures
- MolScript: The Official Web Site
- Center for Molecular Modeling
- Links to Modeling Software
- Motif3D Input Page
- Running MICE as an embedded applet - MICE
- Protein Morpher
- PyMOL Home Page
- XdomView: Visualize protein domains and exon structure
F. 2-D PROTEIN GELS
- Partial List of Web 2D Electrophoretic Gel Databases
- ExPASy - SWISS-2DPAGE top page
- 2D PAGE Databases
- NCI Catalog of 2D PAGE gel images found in Web databases
- Compare Gel Images with Flicker at NCI
G. PHYLOGENY
- PhyloBLAST
- Phylogenetics and Evolution Menu
- Large List of Phylogeny Programs
- WebPhylip
- PhyloDraw: a drawing tool for creating phylogenetic trees
- Oxford University Evolutionary Biology Group - Software
- ATV - a phylogenetic tree display tool
- treealign
- Weighbor (Weighted neighbor joining)
- fastDNAml (DNA phylogenetic trees)
- TreeView Phylogeny Software
- SHOT - Shared Ortholog and Gene Order Tree Reconstruction Tool
- [ RIO SERVER ]
- AllAll (Alignment, MSA, Probable Ancestral Sequence)
- ETH: CBRG
H. PROTEIN SITES - UNSORTED
- BLIMPS (BLocks IMProved Searcher)
- CUTTER: A tool to generate and analyze proteolytic fragments
- Enzyme Nomenclature
- Codon Usage Database for Different Species
- PatSearch
- Kangaroo pattern search
- Superfamily: for sequence search and alignment
- SWBIC - BLAST Filter
- InterProScan
- BIND - The Biomolecular Interaction Network Database
- NetPhos 2.0: Predict phosphorylation sites
X. PROTOCOLS, TIPS AND CALCULATIONS
- Lab Protocols- quick index
- Lab. Protocol 1
- bioProtocol
- metazoa > your online protocol system
- BIOVISA.NET -- Online Protocol, Journal and Forum Center for Life Science Researchers
- Molecular Biology Protocols
- Molecular Biology Shortcuts - Protocols
- NWFSC Molecular Biology Protocols
- Wash U Mol Biol Protocols
- Technical Tips at BioMedNet
- Methods: A Companion to Methods in Enzymology
- Interactive Statistical Calculation Pages
- NIST Chemistry WebBook
- SciWeb - The Life Science Home Page
- PCR optimization | molbiol.ru
- Gel Electrophoresis Simulator
- CentrifugeHelper Version 1.1
- BIOVISA.NET -- Online Protocol, Journal and Forum Center for Life Science Researchers
XI. MOLECULAR BIOLOGY SOFTWARE (mostly free)
- AiO - DNA/protein programs and oligo management
- The BioCatalog of Software
- Huge Database of Molecular Biology Software and Online Tools at Genamics
- GeneDoc HomePage
- BioEdit Sequence Alignment Editor for Windows 95/98/NT
- EnzymeX - Restriction site analysis (Mac only)
- Free Molecular Visualization Software
- Protein Explorer FrontDoor
- CodonAlign
- Educational Software for Biotechnology
- Free Software for Mac and PC
- List of Software for molecular biology
- Genotator
- BOXIT - Database for Molecular Biology Laboratories ($)
- JaMBW: Java Molecular Biology Directory
- MOLMOL - MOLecule analysis and MOLecule display
- PaperWorks paper organizer
- PC Software for Molecular Modeling
- pDRAW32 - DNA cloning, sequence analysis and plasmid/DNA plotting
- PHYLIP Software for Phylogenetics
- PhyloDraw: a drawing tool for creating phylogenetic trees
- RasMol Home Page
- SEQtools downloads
- SeqVerter: Sequence Format Converter
- SeqVu-DNA sequence software (Mac only)
- The Sanger Institute : Software
- Software from TIGR
- Software for computational molecular biology
- StuffIt Expander: Unzip zip, access StuffIt files, free
- Sequence Analysis for Mac OS X
- TreeView Phylogeny Software
- TREE-PUZZLE 5.0
- Visual Molecular Dynamics--3D Graphics
- WU BLAST at Wash U.
- Affordable biocomputing for everyone
- Apollo User Guide
- Apollo Genome Annotation Tool
- Handy Online Utilities at JustBio
- Uniblast
- ClustalX (download)
- Jmol: Molecule viewer
- Tools at Penn State Bioinformatics Group
- Software Tools - The Institute for Genomic Research
- Sweet2: Saccharide structure utility
- MatchMiner Home Page
- Alfresco: Comparative genome visualization tool
- Home page of ANTHEPROT
- Biolinux: Genomics Software
- Welcome
- Software for kinetics
- ACGT
- GeneMine: Free at last!
- DNATools
- Librarian - create full featured virtual PDF library
- linkage software list (page 1)
- Molecular Evolutionary Genetics Analysis
- DARWIN: Data analysis and retrieval of protein, nucleic acid
- Artemis: genome viewer and annotation tool
XII. BIOINFORMATICS TOOLS
- Search Bioinformatics Sites with BioinfoBot
- Bioinform - The Global Bioinformatics News Service
- CuraToolsTM - Home Page
XIII. MICROARRAYS
A. INTRO TO MICROARRAYS
- Intro to Microarrays
- Microarrays-Introductory Factsheet
- DNA Microarray (Genome Chip) (by Leming Shi, PhD)
- Microarrays, their application and the standardisation of their data
- Papers on Microarray Data Analysis
B. MICROARRAY DATABASES
- Microarray Database at EBI
- Gene Expression Omnibus Home
- PubGene Expression Data Analysis Tool
- The Stanford Microarray Database
- Gene Expression Atlas: Text Query
C. MICROARRAY LINK LISTS
- GoMiner: interpret "omic" data
- MatchMiner Home Page
- microarrays.org - your public source for microarraying information, tools, and protocols
- microarray
- Microarray Links at UCLA
- Web resources on Gene Expression and DNA Microarray Technologies
- GRID IT: Resources for Microarray Research
- Microarray Citation Electronic Library
- MicroArray Explorer Tool for Data Mining
D. SOFTWARE AND PROTOCOLS FOR MICROARRAY
- NIH - DAVID
- longhorn array database
- EBI Microarray Tools - Expression Profiler
- SMD Microarray Resources : Software & Tools
- Microarray software comparison
- CAGED Cluster Analysis of Gene Expression Dynamics
- BASE: BioArray Software Environment
- GAAS: Gene Array Analyser Software
- GenMAPP Microarray Software
- Free Microarray Software from Mike Tyers
- Statistical Analysis of Microarray Data
- OligoPicker Homepage
- Intelligent Systems and Bioinformatics Laboratory
- GeneSifter.Net?? - Microarray Analysis Online
- cDNA Array Protocols