Multiple Sequence Alignment
April 2nd 2008
Below are a list of files and sequences that are useful when working
through some of the exercises presented during the teaching
The two files below are the same sequences you were provided with
printed on paper and that you had to align by cutting them out and
using scissors to insert gaps in appropriate places.
To check your answer, you could try downloading these files, and
aligning them automatically (for example useing the MUSCLE webserver at
Alternatively, try loading the sequences into a text editor - you can
try out the same exercise you carried out using scissors and paper in
the editor, simply using the "-" key to insert gaps where appropriate.
Sequence set A
Sequence set B
EBI MUSCLE webserver
Manual Adjustment of Automatica MSAs
You are asked to try using a combination of CLUSTALX and SEAVIEW to
identify and correct errors in the set of alignments given below.
The errors included in the alignments are all created by automatic MSA
software - in most cases by CLUSTALX. In addition to these
error-containing alignments, reference "correct" alignments are
provided from the Balibase alignment reference set. The alignments in
Balibase contain regions in which structural superposition confirms the
accuracy of the alignment, and can be used as a training set/gold
standard for MSAs.
BALIBASE CLUSTALX PRANK MAFFT PROBCONS
Build your own MSA
Try looking for 14-3-3 motifs (browse ELM
to learn more about the motif) in RAF1_HUMAN
using MSAs built by searching for sequences either on the EBI protein BLAST server.
Try the same thing looking for MAP Kinase interaction sites in the
to Gibson Team course pages at EMBL.