General informatics "lecture"

This is a self-guided lecture whose purpose is to introduce you to internet resources for information about genetics and genomics. Some of these are general sources of information. Others are much more specialized. I recommend that you just go through the four web pages and check each of the links in turn to see what resources it has to offer. These pages are constantly being developed, but the current status is suitable for an informative tour.

Homeworks 1 and 2 have questions that can be answered using the online resources presented on these pages.

In these examples, the LXR gene and protein will be used to illustrate the various informatics resources. This is just a way of showing how they all present information that can bear on a gene and its function. In 2007 a paper on LXR appeared in Nature: Mitro et al. "The nuclear receptor LXR is a glucose sensor." 2007. Nature 445 , info:doi/10.1038/nature05449. (Nature, PubMedID: 17187055)

General information (page 1):
Library (Research Port) (CBMG librarian's guide to resources, a dynamic page with audio made using Captivate).
Google (scholar, blogs, books)
Wikipedia
Faculty of 1000
Scitable
Bookmarks (Connotea, delicious)
RSS feeds (updated information from news sources; an example)

National Center for Biotechnology Information (page 2):
Entrez NCBI has many databases. Entrez searches all of them at once. Note PubMed, books.
PubMed
      details and URL,
      limits,
      email alerts;
      use the link feature to go between databases
OMIM (online Mendelian Inheritance in Man)
NCBI sequences and sequence-based searches (nucleotide and protein databases)
      Sequence file formats
      File format toggling with display
      Blink (sort by taxonomic group, other features)
      Refseq: (handbook, accessions) and Gene
BLAST

Genomics Resources (page 3):
EBI, including Ensembl
UCSC browser
Protein Information Resource
Model Organism Databases

Courses and other collections of resources (page 4):
      My own bioinformatics links, a page full of one-click links (with no explanation)
      biowiki, the Biodirectory wiki BioWiki is "a unified gateway to store, search, and retrieve and update information about life sciences research web resources."

An entire course on "practical bioinformatics" online: BIOL439 at Penn State.

tools
A collection of online analysis tools maintained by Dr. Andrew Kropinski, Queen's University Public Health Agency of Canada's Laboratory for Foodborne Zoonoses in Canada (molbiol- tools.ca).