The tools at our disposal:
National Center for Biotechnology Information
What does NCBI do? Established in 1988 as a national
resource for molecular biology
information, NCBI creates public databases, conducts research in computational
biology, develops software tools for analyzing genome data, and disseminates
biomedical information - all for the better understanding of molecular processes
affecting human health and disease.
http://www.ncbi.nlm.nih.gov/
CLC Free Workbench
A Free Workbench for basic bioinformatics
CLC Free Workbench creates a software environment enabling users to make a large
number of bioinformatics analyses, combined with smooth data management, and
excellent graphical viewing and output options.
The software package is a community edition, available for Windows, Mac OS X, and
Linux. Download is free of charge.
http://www.clcbio.com/index.php?id=534
ProtParam tool (References / Documentation) is a tool which
allows the computation of various physical and chemical
parameters for a given protein stored in Swiss-Prot or TrEMBL
or for a user entered sequence. The computed parameters include
the molecular weight, theoretical pI, amino acid composition, atomic
composition, extinction coefficient, estimated half-life, instability index,
aliphatic index and grand average of hydropathicity (GRAVY).
http://ca.expasy.org/tools/protparam.html
OK INBRE Bioinformatics Bulletins
http://microgen.ouhsc.edu/bioinfobulletins/
MOLO: The Molecular Logic Project and the Molecular Workbench Project
The goal of the Molecular Logic project is to improve the ability of
all students to understand fundamental biological phenomena in
terms of the interactions of atoms and molecules. The Molecular
Logic project aims to do this by enhancing biology courses with
guided explorations of powerful atomic and molecular
computational models. These models are embedded in an easily
implemented database linked to both typical textbooks and standards.
http://molo.concord.org/ http://workbench.concord.org/
Pedro's BioMolecular Research Tools
A Collection of WWW Links to Information
and Services Useful to Molecular Biologists
http://www.public.iastate.edu/~pedro/research_tools.html
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.
First time users: please register for a free account.
http://workbench.sdsc.edu/
The Lycoming College Macromolecular Modeling and
Bioinformatics Page
http://srv2.lycoming.edu/~newman/models.html
Dolan DNA learning center at Cold Spring Harbor (DNAi)
http://www.dnalc.org/home.html
http://www.geocities.com/bioinformaticsweb/
Oklahoma City community college site
http://Microgen.ouhsc.edu/
www.doegenomes.org (genes gateway and HGP)
The Gene Gateway Workbook
A collection of activities derived from the tutorials at Gene Gateway, a guide to
online data sources for learning about genetic disorders, genes, and proteins.
http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/ggworkboo
k1.pdf
Important organisms and vectors to be able to find:
E coli bacterium genome: AE005174
Bacteriophage lambda: NC_001416 (find with cloning vector puc19 complete sequence)
pUC19 cloning vector: M177789 (find with cloning vector puc19 complete sequence)
pAMP, pKAN, pBLU seqs are found in:
www.dnalc.org/ddnalc/resources/plasmids.html
The latter sequences have been saved in the bioinformatics folder, as well (stripped and
numbered)