MLML Computer Lab Instructions Logging in and using the Windows XP machines in the Moss Landing Marine Labs computer classroom.
     
Alu Bioinformatics Extension This computer follow-up to the Alu PV92 PCR Lab allows students to repeat their experiment "in-silico" and leads to an exploration of ethics in bioinformatics.
     
The National Center for Biotechnology Information including Entrez.
We could spend the whole course on this one site.  The National Center for Biotechnology Information is more of a "bioinformatics" site than a "biotechnology" site, but the name of the center predates the common usage of the word "bioinformatics."  
     

NCBI ORF Finder

This server returns all six reading frames from your DNA sequence... the good thing is that it also allows you to pick a variety of unusual genetic codes in addition to the standard.  
     

Whales & Hippos
Bioinformatics

Working with DNA
Bioinformatics

Collection of bioinformatics activities related to the biotechnology portion of this course.
     
science.bio.org This website sponsored by the Biotechnology Industry Organization collects and disseminates breaking news stories from the scientific media. Ideal for high school and college undergraduates with some background. Endorsed by the California State University Program for Education and Research in Biotechnology.
     
DNA Toolkit This software will create double-stranded, inverse, complemented versions of your input DNA. It will also translate your DNA and reverse translate your input protein sequence.
Thanks to R. A. Bowen at
     
     

NCBI Blast

Our Blast Help Page

Blast Education

Sequence alignments provide a powerful way to compare novel sequences with previously characterized genes. Both functional and evolutionary information can be inferred from well designed queries and alignments. BLAST 2.0, (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases. Since the BLAST algorithm detects local as well as global alignments, regions of similarity embedded in otherwise unrelated proteins can be detected. Both types of similarity may provide important clues to the function of uncharacterized proteins. Take a course on Blast!
     

NCBI Cn3D

NCBI Structure Database

Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.
     
Webcasts From time-to-time we hold webcasts to support a particular High School class.  Access those webcasts through this link.  
     
     
NCBI
Molecular Modelling Database
NCBI's structure database is called MMDB (Molecular Modeling DataBase), and it is a subset of three-dimensional structures obtained from the Protein Data Bank (PDB), excluding theoretical models. The database is considerably smaller than Entrez's protein or nucleotide databases, but a large fraction of all known protein sequences have homologs in this set, and one may often learn more about a protein by examining 3D structures of its homologs.
     
Chromas Chromas is software that allows one to look at raw output from an automated sequencer. It can export it to FASTA format files for use in Blast searches.
     
Reverse
Complement
Tool
Copy and paste your nucleotide sequence into this window, hit enter, and it returns the reverse complement of your sequence. Just copy and paste that sequence into a new file that includes "rev_comp" in the name.  
     
Protein Data Bank The PDB is the main worldwide repository for three-dimensional structure data for biological macromolecules.
     
ImageJ from the NIH This software is excellent for a wide variety of applications. In this class we use it to prepare digital traces of scanned gels.
     
MDL Chime You will need this plugin to run "Protein Explorer" on the "Internet Explorer" browser.  It is provided free by a software company called MDL.  You do have to go to their website and register in order to get the free copy.
     
Protein Explorer from
Eric Martz and
the NSF
This website turns your browser into a powerful 3-D protein modelling application.
     

Human Genome Project
at the UCSC Center for
Biomolecular Science
and Engineering

The International Site for the Human Genome Project
at the US Department of Energy

The Human Genome Project is an international effort begun in 1990 to determine the sequence of the approximately 3.2 billion subunits that make up our DNA. The UCSC Center for Biomolecular Science and Engineering (CBSE), led by David Haussler, is one of 19 centers around the world that make up the International Human Genome Mapping Consortium, a crucial component of the Human Genome Project.

Over the past decade, genome centers all over the world generated the raw sequence information by determining the sequence of the DNA subunits (bases) of small fragments of human DNA. Jim Kent, a Reseach Scientist at UCSC and a member of the UCSC human genome team, wrote a program that assembled the sequenced fragments , creating a working draft sequence that spanned all 23 human chromosomes. UCSC was the first site to post the assembled human genome sequence on the world wide web, distributing it freely, without any restrictions on use.

The Center for Biomolecular Science & Engineering at UCSC - Outreach Page The student outreach and diversity programs sponsored by the UCSC Center for Genomic Sciences and coordinated by Phoenix Eagleshadow are available here.  
     
UCSC Genome Bioinformatics This website contains the tools UCSC's scientists have developed to explore and analyze the vast amounts of data being generated from several major sequencing efforts, including the human, chimpanzee, mouse, rat, chicken, Fugu, Drosophila, C. briggsae, C. elegans, yeast, and SARS genomes. The computer programs available include browsing, sorting, identification, and graphical visualization tools.
     
Joe Felsenstein's Phylogeny Resources including Phylip These two sites contain everything you could ever want in terms of taxonomical software.  Reconstructing phlyogenies is a statistical, not an exact science.  Therefore, the more different methods support a given network, the more likely the network is to be real.  In other words, if you want your paper published you better have agreement from at least three of the programs contained in Felsenstein's list!
     

ClustalX

ClustalW

ClustalW
alignments
on the web
(BioWeb Pasteur Institute)

Clustal X is a new windows interface for the ClustalW multiple sequence alignment program.

Clustal W is a general purpose multiple alignment program for DNA or proteins.

Another place to download ClustalX.

     
ExPASy Proteomic s Server
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. It contains the SwissProt Database as well as many other important resources.
Molecular Biology Tools OnLine This Canadian website (Dr. Andrew Kropinski, Department of Microbiology & Immunology, Queen's University, Kingston, Ontario) is up-to-date (June 2004) and excellent for both the lab sequence jockey and newbie explorers.  
     
Codon Align This is a great little program that aligns DNA sequences according to their protein alignments.  
     
Sequence Extractor    
     
DNA Translation Tools    
     
ReadSeq Does the painful work of converting sequences in the annotated ncbi format to the simple FASTA format.  
     
Bioinformatics Tools at Adelaide    
     
Lesson Plan Assignment Applies only to teachers taking course for graduate credit.  
     

     

Useful Links - Sites that may be useful for teaching about Biotechnology and Bioinformatics

 

Useful links - Sites that may be useful for teaching about marine science research are listed:

     
     
U Wisc. BioLearn U Wisc BioWeb Biology Workbench
Swiss PDB Viewer Affordable Bio Software (TIBS) BiowareDB
SeqLinks PredictProtein Server ProteinStructurePrediction
SwissModel Perl Scripts Evolution
   
Lessons Woodrow Wilson National National Fellowship for Teachers
     
     

Inquiry-based Marine Biotechnology and Bioinformatics for Teachers
Simona Bartl and Henrik Kibak
June 20 - July 8, 2005 - Moss Landing Marine Laboratories

Please direct comments to:

Simona Bartl sbartl@mlml.calstate.edu
Henrik Kibak henrik_kibak@csumb.edu