Future Monday and Wednesday classes will take place in CB 206!
Assignments for Friday's class:
Assignments for Monday's class:
NCBI (National Center for Biotechnology Information) is a home for many public biological databases (see diagram below). All of the databases are interlinked, and they all have common search and retrieval system - Entrez.
A list of the different databases in ENTRZ is here.
Search Field Tags- Listed here.
Explore features of Entrez interface: Advanced Search, Index,Clipboard and MyNCBI.
Other Useful Databases and Services:
While Medline is incorporating more and more non-medical literature, there might still be gaps in the coverage. Alternatives are other databanks available though the National Library of Medicine (here) and the local services offered at the UConn libraries. Especially Current Contents and Agricola nicely complement PubMed. The best way to access them is through the UConn library's website. In particular, the "Web of Science" database gives access to the Science Citation Index: a database that tracks cited references in journals.
Note that many resources are restricted to the UConn domain, thus you either need to access them from a campus computer or through the proxy account. In some instances you are prompted to connect to the UConn VPN network or through EZproxy (the latter is new, and not all links have migrated to using EZproxy).
If you want to be informed about new sequences/articles in your research area? Check out these services (- you also can use MyNCBI for this, but I use Pubcrawler for several years and it works reliably):
In searching Entrez, you can add links to online journals for which UConn has a subscription. (If you are outside UConn, you need to set up a proxy account for the links to work).
The link to use is http://www.ncbi.nlm.nih.gov/sites/entrez?otool=uconnlib
Do example on clipboard and index. (use GI 2266989 (nucl) and 3334404 (prot))
Other web pages:
Nucleic Acid Research Database Issue
|Sequence and structure databanks can be divided into many different categories.
One of the most important is:
One problem in maintaining databanks is "owner ship" of sequences, which in many databanks prevents a continuous update of sequences. Even is errors are detected, they are not easily removed form the databank. E.g. ATP synthase operons in E.coli see http://mic.sgmjournals.org/cgi/content-nw/full/156/7/1909/F1
ORF finder illustration of ORFs
ATPsynthase ORF as query in databank search (BLink):
Alternative ORF as query in databank search:
Alternative ORFs in BLink