A Brief Bioinformatics Tutorial

An approach to what can be accomplished in Silico


Introduction Sequence Structure Function

Quickly Exploring Your Gene In The Literature: The iHop Server

iHOP means information Hyperlinked Over Proteins. The iHop server is a very efficient tool allowing finding all the papers in which a particular gene name is cited. Let's try it:
1/ Go to the Web site
2/ Type a gene name (e.g. vps36) or an accession number (e.g. UniProt or NCBI Gene, etc.) into the search field in the menu bar.

3/ In many cases your search term will correspond to various genes or proteins. Click on the "paper" icon on the right-hand side to select the corresponding gene. When you mouse goes over it, it should be written "interaction information for this gene"

4/ The "interaction information" contains all sentences found in the literature for the main gene of a page (gene A) in red, and other genes (gene B) in Blue. Gene symbols within sentences are hyperlinked. Therefore, clicking on a gene symbol (e.g. gene B) will bring you to the page of gene B.

5/ A nice option is the Enhanced PubMed/Google query. Each gene page contains at the top a link to execute it. These queries allow you to quickly query PubMed or Google for a specific gene including all its synonyms and orthographic variations.
6/ You can also tune your iHop navigation, just use the Filter and Options link in the menu bar to change overall appearance parameters.

More detailed/complete information about iHOP can be found by clicking on "help".

More Functional Information at NCBI

Up to now, we used "NCBI protein", if you select "NCBI gene" , you will see that you actually have access to plenty of extra-information such as interactions.
1/ So, go there ,
2/ Type in .. do I need to tell you ;) ?
3/ Select the good gene,
4/ Look at all this information!

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