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Alignment Assignment Many resources for multiple sequence alignments are now available on
line. http://cnx.org/content/m11026/latest/
has a great deal of information about BLAST as well as a tutorial. http://pbil.univ-lyon1.fr/alignment.html
has a list of available alignment software. Several sites actually have the tools available for doing the
alignments on line. All that you have
to do is upload a FASTA file, and the computer running the web site will do
the alignment. These systems use
different methods to align these sequences, so many will produce different
alignments from the same input file.
We want you to try a number of these programs on your own time, and
investigate the results. I have prepared a FASTA file of partial calmodulin
sequences from ten species of Conus. This is a really cool genus of predatory
tropical reef snails with beautiful shells and complex cocktails of oligopeptide toxins.
Calmodulin is involved in the release of
these toxins. These sequences were put
on genbank by T.F. Duda
Jr., but never published. Download the file from http://ib.berkeley.edu/courses/ib200a/sequences.fasta.
Go to the following web sites and generate alignments of the
sequences. Browse for the appropriate
file on your computer and push align. You
may have to set the output format to something that you know you can use,
such as FASTA or Clustal. It may take a few
seconds, when it is done download the alignment files that the program
generates. In some cases you will have
to copy the alignments from web pages to text files. Additional information
about the alignment methods is available on the web sites. http://bibiserv.techfak.uni-bielefeld.de/dialign/submission.html http://baboon.math.berkeley.edu/mavid/ http://align.genome.jp/
- this web site has three different available methods of alignment, ClustalW,
MAFFT, and PRRN. You should generate a
separate alignment using each of these methods. Once you have these alignments make the following observations for
each alignment, write them down and turn them in to me: 1) Visually inspect the output in Macclade,
Clustal, Winclada or 2) Record the total number of characters in the aligned matrix. 3) Record the number of parsimony informative and uninformative
characters (use Mop Uninformative Characters in Winclada
or a similar command in MacClade. PAUP* and 4) Save the matrix in the appropriate format and run a parsimony
analysis in Winclada/Nona, PAUP* or PHYLLIP. This matrix is small enough for you to run
an exhaustive search. 5) Record the number of minimum length trees found, and the number of
steps they have. 6) Make a strict consensus tree and note the resolution. Are the
consensus trees from the different alignments all compatible? If not, where do they conflict with each
other? (Make sure that you root the trees with the same taxon
for doing this comparison.) In a couple of weeks we will be going over many of the options
available for these programs in lab as well as running POY, which generates
trees and alignments together. |
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