Integrative Biology 200A
University of California, Berkeley
"PRINCIPLES OF PHYLOGENETICS"
Lab 3: GenBank and Sequence Alignment
Today we will examine three tools that are useful for obtaining and preparing
molecular sequence data for phylogenetic analysis.
GenBank is the NIH sequence
It is can be accessed, searched, etc. on the internet and contains sequence data
for over 100,000 species.
Jalview is a multiple alignment editor written in Java, so it will
work on PCs or Macs.
It was developed by Andrew Waterhouse, Jim Procter, David
Martin, and Geoff Bartonand is freely available on the web (http://www.jalview.org/).
number of other alignment programs are available both for free and at a cost, and for all
major computer platforms. And the third tool is your old friend Mesquite. You can also
experiment with MacClade if you have time and want to.
First, we’ll try out some of GenBank’s functions.
Open Internet Explorer on your
computer and go to the site http://www.ncbi.nlm.nih.gov/.
This is the National Center for
Biotechnology Information website, where GenBank (among other things) resides.
At the top of the page, you will find a blank where you can begin searching.
down the ‘All Databases” menu and select ‘Nucleotide’, GenBank’s DNA/RNA
Try typing in the name of your favorite taxon in the search bar to see
if there are sequences for it.
Once you’ve done this, a list of sequences will appear (if
there are sequences for your organism). You can also search for by taxon using
‘Taxonomy,’ and see all the sequences available for a given genus, family, etc. Each
sequence is listed by its accession number, and information about the taxon, gene, etc. is
Follow the link for one of the sequences you’ve found.
A new page with
various information about the authors of the sequence, the taxon, gene, where it was
published, etc. will appear.
At the bottom of the page you will find the sequence itself.
Near the top of the screen, you can see that there are several options for displaying and
saving the sequence.
Check out some of the display options (choose them from the pull-
down menu and then push display), but don’t bother saving anything for now.