![[rrna]](im/liccal.jpg)
![[ssu]](im/small_subunit.gif)
![[lsu]](im/large_subunit.gif)
Please note: This page has not been completely updated for some time
Search WWW
- Excite Search
- AltaVista Search
- Lycos Search
- Yahoo - Science:Biology
- AltaVista Search
Molecular Biology Searches
- NCBI General GenBank Search
- NCBI's Entrez
- NCBI Taxonomy Browser
- Basic Blast Search
- FASTA Programs at Univ. of Virginia
- PubMed Search
- Entrez PubMed Query
- Search and Alignment Tools Tutorial
- NCBI GenBank Query Email Documentation
- Swiss Protein Site
- EMBL Tools
- EMBL Home
- PredictProtein Email Service
- Brookaven Protein Data Base
- Bioinformatics Databases and Analysis Services
- Pedro's BioMolecular Research Tools
- Blast Search at Cambridge University
- GeneStream Search Site (France)
- MBCR Links to Sequence Analysis
- Brookhaven National laboratory Biology Page
- EBI's Scanps Search Server
- SpliceOme Relational Database for Intron-Exon Boundaries
- About Inteins
- NCBI's Entrez
- Back to Top
Sequence Alignment
- EBI's ClustalW Alignment Web Server
- EBI's ClustalW Online Help with Commonly Used File Formats
- VSNS Multiple Alignment Links
- BCM Alignment Launcher
- HMMER Alignment Software Server
- Useful Hyper-Article on HMMER and Multiple Alignment by Sean Eddy
- Browse PFAM Alphabetical Collection of Protein Alignments (Constructed with HMMER)
- Download 1998 PDF Article on 1313 PFAM Alignments of Proteins
- AMAS Server (Multiple Alignment of Protein Sequences)
- AllAll: Related peptide sequences
- Protein Sequence Alignment -- Prof. Barton at EBI
- SAM: Sequence Alignment and Modeling System
- Jalview - Java Multiple Alignment Editor for Unix or Windows or View Screenshots
- Web Alignment Query (of Two Sequences)
- ClustalX Alignment Software FTP Site
- DCSE Alignment Software for Unix or DOS
- BLOCKS Web Server (Fred Hutchinson Cancer Research Center in Seattle)
- CINEMA 2.1 Alignment Software for Unix or DOS
- Listing of Protein Alignment Programs
- Alignment programs for Sun (Gopher)
- MALIGN/POY Site (FTP)
- Basics of Multiple Alignment (VSNS)
- Molecular Biology, Strings, Sequences, Trees, Maps - Lloyd Allison
- EBI's ClustalW Online Help with Commonly Used File Formats
- Back to Top
Ribosomal RNA
- Ribosomal Database Project II
- Robin Gutell's RNA Secondary Structure Diagrams
- RNA Structure Primer
- Yeast tRNA-Phe Structure or Here (Requires Chime Plugin)
- The RNA World
- RNA Base
- Michael Zuker's RNA Website
- Zuker's MFold Server
- Vienna Web Interface to RNAfold Program
- Tinoco Plot Web Interface
- Rnadraw RNA Folding Program for Windows
- RNA Sequence Editor DCSE Program for Unix or DOS
- RnaViz Drawing Program for Linux or Windows (DCSE Format)
- Vienna RNA Folding Program for Unix
- ESSA RNA Folding Program for Unix
- Rod Page's Listing of RNA Folding Programs
- DOGMA: Dual Organellar GenoMe Annotator
- Robin Gutell's RNA Secondary Structure Diagrams
- Back to Top
Protein Structure
- ExPASy Protein Site in Geneva
- ExPASy Protein Search
- Protein Databank (PDB)
- Beginner's Interface to PDB Searching
- Protein Structure Course (Password Protected) or 1997, or 1996 Courses Here for Free
- The Principles of Protein Structure using the Internet
- Protein Crystallography 101
- Portions of a Ph.D. Dissertation on Protein Crystallography
- The ProDom protein domain database
- GDP - Genome Database (Protein Info/Searches)
- Interpro Resource for Genomic Proteome Comparisons
- Article: Seven Ways of Looking at a Protein
- CPE Protein Structure Prediction
- The AAA Protein Superfamily Server
- Jpred - Consensus Protein Secondary Structure Prediction
- Download RasMol and Related Resources
- Download MolView Lite for Macintosh
- Image Summarizing Protein Synthesis in Eukaryotes
- ExPASy Protein Search
- Back to Top
Mitochondrial Genomes
- Mitochondrial Genomics Source Guide
- NCBI Organelle Genome Resources
- NCBI Metazoan Mitochondrial Genomes as Unranked Classification
- NCBI Metazoan Mitochondrial Genetic Codes
- OGMP Organellar Genomics
- OGMP Listing of Mitochondrial Genomes Sequenced
- GOBASE Organelle Genome Database
- C. elegans Genome Project Mitochondrial Directory
- Origin and Nature of Mitochondria
- Software and Publications by Mathieu Blanchette and Colleagues
- NCBI Organelle Genome Resources
- Back to Top
Primer Design
- PCR Overview
- PrimerDesign Documentation
- Tm Determination
- Whitehead Institute's Primer3 Web Server
- CODEHOP: COnsensus-DEgenerate Hybrid Oligonucleotide Primers (Web-based)
- The PCR Primers Database
- Long PCR Protocol
- Primer/Oligo Design programs for Macintosh
- Apple Pi:Primers! Software
- Listing of Primer Software
- Listing of Mac Primer Software
- Invitrogen's Oligo Calculator
- Biowire.com's free Jellyfish software (for Windows) Now Includes Oligo Design Options
- PrimerDesign Documentation
- Back to Top
Restriction Enzymes
- How Restriction Enzymes (RE) were Discovered
- Webcutter On-line Tool for Restriction Mapping
- RE Overview
- Multi-Cut Database of RE Buffers
- GCG's Mapsort Utility
- Webcutter On-line Tool for Restriction Mapping
- Back to Top
Transposons
- Molecular Mechanisms of Recombination
- Transposons: Mobile DNA
- Animated Transposition (Requires Plug-in)
- Walbot Lab
- Mobile Genetic Elements
- Transposons: Mobile DNA
- Back to Top
Genomics
- Genomes On-Line Database (GOLD)
- Genomics at NCBI
- Genomics at EBI or FTP Site for Eukaryotes
- ENSEMBL
- Genomic Information for Eukaryotic Organisms (euGenes)
A Quick Guide to Sequenced Genomes - Genomics at NCBI
Evo-Devo
- The Homeobox Page
- Homeotic Genes Explained
- Cool Views of Drosophila Homeotic Proteins and Their Expression
- Xenopus Molecular Marker Resource
- Winged Helix/Forkhead transcription factors
- Cnidarian Homeoboxes and the Zootype
- Sean Carroll's Lab Page
- FlyBase, FlyView, FlyLab, FlyBlast, NCBI's Drosophila Genome Page, FlyGenome, Image Database of Gene Expression Patterns in Fly, FlyChromosomes, FlyBrain, or the Interactive Fly,
- Boston Evo-Devo Resources
- Evo-Devo Articles by Taxon or Concept
- Evo-Devo Learns a Larval Lesson
- Developmental Mechanisms Problem Set
- HOX-Pro Homeobox Genes Database
- Berkeley's New Evo-Devo Center
- How Limbs Evolved From Fins
- How Insects Lost their Legs
- Scott Gilbert's Evo-Devo Course
- Free Downloads of Evo-Devo Articles in PNAS
- Homeotic Genes Explained
- Back to Top
Phylogenetics
- Felsenstein's Directory of Phylogeny Programs
- Tree of Life List of Phylogeny Programs
- PAUP* Website, Quick Start Tutorial V. 1 (.pdf Format), Command Reference Doc V. 2 (.pdf Format)
- Tutorials for PAUP*, Clustal X, etc.
- Likelihood-Based Tests of Topologies in Phylogenetics
- MrBayes (Phylogenetic Analysis Program using Bayesian Inference) - See also: 1 - 2 - 3 4 - 5 - 6 - 7 - 8 - 9 - 10
- IUBio Software and Data
- IUBIO Molecular Biology Mac Software
- Univ. of Glasgow Systematics Software Listing
- Download Component 2.0 (Windows) Now Free
- Software Listing from Paul Harvey's Group at Oxford
- Gogarten and Lewis Course on Computer Methods in Molecular Evolution
Paul Lewis Course on Phylogenetics- Workshop on Molecular Evolution Schedule and Lectures
Likelihood Ratio Test- Natural History Museum's Molecular Systematics and Evolution of Microorganisms
- Programs for Phylogenetics and Population Genetics
- Sequence Analysis Tutorials
- VSNS HyperText Coursebook Chapter on Molecular Phylogenetics
- Genetics Computer Group (Wisconsin GCG)
- Wisconsin GCG Tutorials
- Codon Usage Tabulated from GenBank (CUTG)
- AnnHyb Sequence Utility Software for Windows
- Ziheng Yang's Program, PAML: Phylogenetic Analysis by Maximum Likelihood
- Pittsburgh Supercomputing Center Sequence Analysis Programs Installed
- Oxford Molecular Group's (GCG, SeqLab)
- Download PC Versions of Phylogenetics Programs, TNT, NONA and WINCLADA
- PHYLIP Site
- MEGA Site
- DAMBE Site (for Windows)
- Web and Downloadable Versions of LVB: Reconstructing Evolution with Parsimony and Simulated Annealing
- Paul Lewis's Software including Population Genetics Package GDA
- Paul-Michael Agapow's Software and Scripts
- Barry Hall's Phylogenetic Trees Made Easy Site
- Tree of Life List of Phylogeny Programs
- Back to Top
Macintosh Software Archives
- U of Mich. Gopher to Mac Archive + Mirrors
- U Mich Mac Archive Mirror (ftp)
- INFO-MAC HyperArchive ROOT
- Chemistry software for the Mac
- U Mich Mac Archive Mirror (ftp)
- Back to Top
Selected Molecular Systematics Journals
- Molecular Phylogenetics and Evolution (On-campus Browsing)
- Molecular Biology and Evolution (Abstracts Only)
- Cladistics (On-campus Browsing)
- Bioinformatics
- Evolution (Free Temporary Access)
- Systematic Biology (1998 to Present) or Here for Some Abstracts and Data Sets 1995-99
- Molecular Biology and Evolution (Abstracts Only)
- Back to Top
Bioinformatics and Biocomputing
- What is Bioinformatics?
- Some Basic Molecular Biology
- Molbiol.net Molecular Biology Tools
- Baylor's Database and Search Tools
- San Diego Supercomputer Center (CMS) Molecular Biology Resources
- Bioinformatics Resources
- Bioplanet Links to Informatics Resources on Web
- Internet-based Courses in Bioinformatics
- A Practical Guide to Protein Sequence Analysis
- VSNS BioComputing Division (On-line Courses and Resources)
- Boston University Bioinformatics Program
- Computational Genomics Course at Univ. of Virginia
- Sequence Analysis and Comparison: A Bibliography (Last Updated Feb., 1995)
- Phylogenetic Analysis Computer Programs
- Compute pI/Mw
- WWW Links Related to Viruses
- TIGR Genomic Databases
- TIGR's Links to Genomic Centers
- Baylor's Human/Mouse/Fly Genomic Databases
- Sanger's Links to Genome Centers
- Sanger's Links to Model Organisms
- Agricultural Genome Information
- Access Excellence
- SNAP Program for Synon./Nonsynon. Calculations
- VESPA Program for Amino Acid Frequency Comparisons
- 4Peaks Native Mac OS X Freeware Program for Viewing/Editing Sequence Trace Files
- Genetic Science Learning Center
- Some Basic Molecular Biology
- Back to Top
Evolutionary Biology Resources
- Prof. Eernisse's Links to History of Life
- Prof. Eernisse's Biology 404 Links to Evolutionary Biology
- Lots of Links to Evolution-related Sites
- Time line of Evolutionists (under construction)
- An Introduction to Evolution
- Summaries of Evolutionary Biology Topics
- Willi Hennig Society Homepage
- Galapagos - Charles Darwin Research Station
- Talk.origins Archive Home Page
- EvoTutor
- Prof. Eernisse's Biology 404 Links to Evolutionary Biology
- Back to Top
Commercial Biotech Sites
- Commercial Resources
- Bio Online: Biotechnology: Companies
- On Line Ordering for Biologists/Biochemists
- BioSupply Net
- Company Locator
- Fisher Scientific
- Promega Corporation Home Page
- New England BioLabs
- Qiagen Product Guide
- Amersham-Pharmacia Biotech (North America)
- Invitrogen's Topo-TA Cloning Kit
- Sequencher Software (Gene Codes Corp.)
- Pipetter Repair and Calibration (Southern Instrument Maintenance Co., Arizona)
- Biowire Product/Service Reviews and Free Software (Free Laser Pointer for Registering)
- CSU Northridge DNA Sequencing Facility
- Lark Technology Sequencing Services
- Color Digital Image 8"x10" Prints for $3
FinchTV 1.2, a free cross platform trace viewer - Bio Online: Biotechnology: Companies
- Back to Top
Douglas J. Eernisse
deernisse@fullerton.edu
CSU Fullerton, Biological Science Home Page
The links on this page were last checked on 12/21/00 and last updated on 5/7/06.
If you find broken links or if you find additional cool sites that are appropriate,
please send them and the Web address for this page to Prof. Eernisse.