What is a bookmarklet?

A bookmarklet (or a favelet) is a snippet of Javascript code, stored as the URL of a bookmark (or a favorite) in a web browser. The term is a portmanteau of the terms bookmark and applet. Whether bookmarklet utilities are stored as bookmarks or hyperlinks, they are designed to add one-click functionality to a browser or web page.

Install seeMotif's bookmarklet for IE8 and use it with MAGIIC-PRO

This section demonstrates the procedure of using bookmarklet in seeMotif with screenshots. It is performed on a Window XP system with Internet Explorer 8. The motif mining server used for illustration is MAGIIC-PRO.

Step 1. Go to the homepage of seeMotif

Step 2. Right-click on the bookmarklet

There are three bookmarklets (seeMotif@CSIE.NTU, seeMotif@EE.NCKU and seeMotif@CSBB.NTU) that can be found in the very top of the homepage of seeMotif. They are identical except that the request will be sent to the corresponding mirror site of seeMoitf. Here we use seeMotif@CSIE.NTU as an example. Right-click on it and then click Add to Favorite...

Step 3. Add the bookmarklet as a Favorite

The previous step will bring a Add a Favorite as shown below. The default Name and Create in should be okay. Just click the Add button.

Now you have finished the installation. The next step starts to use it.

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Step 4. Perform motif discovering with MAGIIC-PRO

Go to the homepage of MAGIIC-PRO. You can follow the instructions of MAGIIC-PRO to perform pattern mining on sequences. For this tutorial, do:

1. click Use PSI-BLAST to find homologues for a query protein
2. click [Example of accession number] and then click Submit Query Request button
3. click Submit Discovery Request button

After that, you will see a result page like this:

Step 5. Click the Favorite you just added

Notice that the bookmarklet is invoked, outside seeMotif, right in the result pages of the motif related servers. Select Favorite » seeMotif@CSIE.NTU from the browser menu:

Step 6. If the pop-up blocker is actived

Select Temporarily Allow Pop-ups and re-do the previous step.

After these steps, you will be directed back to seeMotif. The following steps are just like those in regular jobs submissions via the mian page of seeMotif.

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Step 7. Refine the data parsed from MAGIIC-PRO

MAGIIC-PRO reported 1 motif and many potential reference sequences in this case. We just click the seeMotif without any changes.

Step 8. See the results of MAGIIC-PRO in seeMotif

Finally, you will see the results of MAGIIC-PRO in seeMotif, cheers!

Install seeMotif's bookmarklet for Firefox3 and use it with ELM

This section demonstrates the procedure of using bookmarklet in seeMotif with screenshots. It is performed on a Window XP system with Firefox 3. The motif database used for illustration is ELM.

Step 1. Go to the homepage of seeMotif

Step 2. Drag a bookmarklet to the Bookmark Toolbar

There are three bookmarklets (seeMotif@CSIE.NTU, seeMotif@EE.NCKU and seeMotif@CSBB.NTU) that can be found in the very top of the homepage of seeMotif. They are identical except that the request will be sent to the corresponding mirror site of seeMoitf. Here we use seeMotif@CSIE.NTU as an example.

Yes, it is just easy. Now you have finished the installation. The next step starts to use it.

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Step 3. Search motifs in ELM

Go to the homepage of ELM. You can follow the instructions of ELM to search motifs with a protein sequence, which is called Functional site prediction. For this tutorial, do:

1. click server in the top menu
2. fill Enter SWISS-PROT/TrEMBL identifier or accession number: with 'P35835' and then click Submit button

Then wait for a while until the browser is indirected to the result page like this:

Step 4. Click the Favorite you just added

Notice that the bookmarklet is invoked, outside seeMotif, right in the result pages of the motif related servers. Click seeMotif@CSIE.NTU from the browser toolbar:

After these steps, you will be directed back to seeMotif. The following steps are just like those in regular jobs submissions via the mian page of seeMotif.

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Step 5. Refine the data parsed from ELM

ELM reported many potential motifs in this case. We just click the seeMotif without any changes.

Step 6. See the results of ELM in seeMotif

Finally, you will see the results of ELM in seeMotif, cheers!

Supported motif servers via seeMotif's bookmarklet

Currently seeMotif supports the following four web servers (with screenshots of their result pages). The seeMotif's bookmarklet works only in the specific result pages, which contain the required data for invoking seeMotif.

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ELM - Functional Sites in Proteins

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MnM - Minimotif Miner Application Search Page

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MAGIIC-PRO employs a novel combination of intra- and inter-block gap constraints to discover functional long motifs that are interleaved by several large irregular gaps.

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SLiMDisc (Short Linear Motif Discovery) is a method to find shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.