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In this movie, we demonstrate how to use the G-language Bookmarklet.
Le's say you are reading an article in Nature.
and you are interested in the word "hexokinase".
Then, highlight the word with your mouse
and go to the Bookmark Bar of your browser, where G-language Bookmarklet is bookmarked.
now click on the bookmark to start!
G-language Bookmarklet is then immediately called up with nice sound effect and animation.
These arrays of icons in a ring provides links to many biological databases and tools.
You can rotate the ring using your mouse scroll wheels, or with cursor keys (or gestures on your iPhone/iPad)
Now, let's locate the "NCBI" icon to search NCBI Entrez databases with the keyword "hexokinase".
Search result in Entrez is readily displayed in a new ring.
Here you can see the hits in NCBI databases such as PubMed, GEO, CDD, OMIM, and etc.
Let's now select the "Protein" database to retrive the amino acid sequence of "hexokinase".
Then, another ring comes up, this time showing the search results in the "Protein" database.
Hexokinase of Mouse (Mus musculus) seems interesting.
By selecting a specific entry, you are finally directed to the NCBI website for more information.
You can scroll down the page to see the amino acid sequence now.
Now, let's select the sequence to start searching with G-language Bookmarklet again.
G-language Bookmarklet is smart, and knows that the selected text is an amino acid sequence.
So this time, G-language Bookmarklet first queries the sequence using BLAST. This may take a little while.
Then the list of BLAST result comes up, instead of the list of databases.
Now you can select a BLAST result to start querying.
The list of databases then comes up, with the specified BLAST hit as the query.
Selecting EB-eye for example allows searching of EBI using the ID of "hexokinase" sequence in mice.
You can free the ring by moving the cursor away, or by pressing "Esc" key.
When no text is selected when G-language Bookmarklet is started up, it prompts for the query keyword.
Let's say you are interested in the bacteria "E.coli". Here I simply enter "ecoli" as a query.
G-language Bookmarklet contains access to hundreds of bioinformatics webservice tools.
G-language REST Service is a collection of more than 100 tools.
There are tools for Codons, Consensus sequences, Nucleotide composition, and numerous others.
Let's select the category "Codons" for example.
This now lists 19 tools related to codon analysis.
Select "codon_usage" program, to see the codon table of E.coli.
This will redirect to the result page, with codon table image.
Similarly, you can use more than 250 tools in EMBOSS suite.
Let's enter "swissprot:FOXP2_ *" to get amino acid sequences of FOXP2 gene in all organisms.
EMBOSS applications are also categorized with nice icons.
now go to "ALIGNMENT MULTIPLE" to see the conservation of the FOXP2 genes.
By selecting "prettyplot", the server downloads all FOXP2 sequences from SwissProt database,
and aligns the sequences using clustalW software,
and formats the alignment result in a while.
Again, you are redirected to the result page,
showing the alignment result.
Another example.
When reading an article,
you may want to locate biological terms.
In such case,
type "reflect" as a query (or select "Reflect" icon)
This will send the entire page for text-mining.
after a while,
The page resumes, with gene/protein names highlighted in blue.
You can also click on the highlighted terms
to obtain more information
like 3D structure, protein interaction, and etc.
One last demo.
there are several hidden commands in G-language Bookmarklet.
One of it is the "destroy" command
which is quite useless,
but demonstrates the power of bookmarklets.
It literally "destroys" the page that you are viewing
But it demonstrates the power of Javascript.
Bookmarklet is a convenient form of web-based software,
since it does not require any installation or setup.