Using Mesquite as a Sanger sequence database: GenBank numbers

[Wayne Maddison]

We use Mesquite and NEXUS files to manage much of our Sanger sequence data. There's a lot to say about this — and David is better skilled at it than I am — but I'll give a quick intro to recording GenBank accession numbers in your files, where there is a new import feature.

One critical item that we won't discuss here is the Taxon ID code stored for each taxon. This is typically your unique code for the voucher specimen for the molecular data. Having a unique Taxon ID Code is important to enable these and other features.

You can see the GenBank number associated with a sequence in the List of Taxa window in two places. One is in the Has Data In Matrix column:

This column deals with other things (click on the heading to see). You can show such columns for all matrices via List>Show Columns for All Matrices.

The other place you can see the GenBank numbers is the GenBank Number column:

This is the column we'll look at now. 

There are two basic ways to enter the GenBank numbers. You can type or paste directly into the column. (To Paste, don't use the Edit>Paste menu item, but rather the menu in the header of the GenBank # column.)

You can also import a file with the GenBank numbers. That will be described in a follow up message, because this place seemed to resist a single long message...

[Wayne Maddison]

To continue...

Currently two table formats for import are accepted . One is easily editable from the lists returned to you from GenBank:

 

(Note the example at right that you can see by hitting the Example button.)

The other format is one that has headed columns for id (taxon id), and the gene names. After that, each row is a specimen/taxon:

Once you've chosen the correct format for your file, you can either Import the GenBank numbers, or you can delay importing them, but do a survey to see what would be imported were you to import. If you do the survey, details will be put in Mesquite's log. Also, cells in the GenBank # column will become temporarily coloured:

If you hold the cursor over the cell with colours, the explanation area of the window will give an explanation (blue arrow, above.).

You can probably figure out most of the rest on your own by reading the options in the Import dialog box!

The colours of the cells last only while you have the file open; they will be gone the next time you open the file.