Multiple Sequence Alignment

Aidan Budd

Exercises

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

"Hand" Alignment

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 the EBI).

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.

Kinase3_ref5

BALIBASE CLUSTALX PRANK MAFFT PROBCONS


1uky_ref3

BALIBASE CLUSTALX

1thm_ref5

BALIBASE CLUSTALX

Kinase2_ref5

BALIBASE CLUSTALX
 

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 protein STE7_YEAST.


Back to Gibson Team course pages at EMBL.