MuLti Sequence Manager plugin

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MuLti Sequence Manager (MLSM) is a plugin for Firefox which allows quick and easy handling of multiple DNA or protein sequences. It does not offer any analysis but helps to find, manipulate and format the sequences before sending them to the appropriate analysis program (e.g. MEGA5 or similar). It is a fine complement between the public or private nucleotide sequence databases and the analysis software.

The plugin is loaded in the sidebar of the browzer where it stays to accompany you in the research for sequences.

MuLti Sequence Manager

 

How to install

To install it, just follow the instructions:

Step 1: First of all you have to load the html page of MLSM from here. Bookmark the webpage saving it wherever you want. Do this either by pressing the star icon twice or by pressing Ctrl-D key combination.

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Step 2: Once bookmarked the MLSM webpage, open the bookmark library by pressing the boxed star at the right of the address bar, and select the saved bookmark. Expand the properties by pressing “More” and check the “Load this bookmark in the sidebar”. Close the Library window.

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From the bookmark library, locate the saved bookmark and open it. The bookmark will load into the browser’s sidebar.

Have in mind that this plugin is at beta version. Although, no support is provided by the author, any comment that will potential lead to the improvement of the code is desirable. Because of the “beta” status of the code, the user has the fully responsibility to check the output sequences. In case you want to address any comment to the author of the plugin, use the email mtrantas at gmail.com.

Installation video instructions

 

Instructions for use

mlsm-sidebarAfter you have succesfully installed the plugin, it should be visible at the left side of the browser. The first line of the plugin is occupied by the title. Immediately after it there is a drop-down menu for selecting the type of sequences you are going to manipulate (DNA or proteins). Nevertheless, this feature is disabled at present and you can only work with nucleotide sequences. Next to the disabled feature there is the button for reseting the plugin. It is useful if you want to clear all the fields and start a new project.

Below lies the main panel of the plugin, where the sequences are imported. For each sequence, there are 2 fields for text, 4 buttons with which you can manipulate the imported sequences and 1 checkbox. The checkbox is used to select which sequences, from those who have been entered in the plugin, you want to export later by pressing the “Create sequences” button. Next to the checkbox there is a text field with the sequence ID (blue arrow). Although an automatic ID is assigned to each sequence, it can be changed to whatever you want. Attention should be taken not to include spaces, as they will be responsible for downstream text conversion errors. Immediately below the sequence ID field lies the main sequence field (orange arrow) where the DNA or protein sequences are typed or imported by “copy & paste”. The plug in has been designed to automatically format the typed or imported sequences. To trigger the automatic formating of the sequences, press left mouse button or touchpad button inside the sequence field.

The four buttons on the right of the sequence ID field can serve to modify the inserted sequence. You can convert the inserted sequence to its reveverse (by pressing the “R” button), complement (by pressing the “C” button), and reverse and complement (by pressing the “RC” button). The “Cl” button is used to clean the inserted sequence.

Every time you want to insert a new sequence, press the buttton “Add new sequences” and a new group of fields and buttons is created. When you have finished with all the sequences, press the button “Create sequences”. All the records with their checkboxes checked are going to be formated in the textfield entitled “Total sequences for export”. Copy and transfer them to the selected program e.g. Blast ot ClustalW2.

 

How to use video instructions

 

Credits

In case you used this plugin and found it useful, give credit by citing the journal article referring to it (link) or at least one of our journal articles.

 

Firefox browser with active sidebar

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