Exercise- Finding Motifs and Conserved Regions

We are going to use the BLOCKS server to extract blocks from an msa, produce blocks
from unaligned sequences and query the BLOCKS database for protein family signatures
using a protein sequence.

• Locate the BLOCKS server web site
• Click the link to the Multiple Aligment Processor
• Upload your .aln file which you produced during the last lesson
• Click ‘Submit’
• In the results window, right-click and save the MAST PSSM file (PSSM =
position-specific scoring matrix)
• Open a new browser window and locate the MAST server web site (on the
MEME/MAST home page you have to select the 2. option to get to the MAST
search form)
• Fill in the form with your email address, upload your MAST file and choose an
appropriate database (e.g. ‘nr’)
• Click ‘Start Search’
• You will receive two emails, the first one telling you, that your job is being
processed and the second one containing your results in html format
• As the MAST search may take a little while we are going to proceed in the
exercise with Block Maker and Block Searcher
• Open the Block Maker search form and provide your query sequences either by
uploading your FASTA file from the third course day or copy the sequences from
a text view at NCBI or a file and paste them into the respective field
• Click ‘Make Blocks’
• Go back to the MSA processor results and click ‘Blocks Format’
• Compare the results of both the MSA processor method (BLOCKS) and the Block
Maker methods (MOTIF and Gibbs sampler)
• You may also make use of the graphical views offered on both pages
• 3D Blocks performs a MAST search of the Protein DataBase (PDB) and displays
a three-dimensional view of the corresponding database entry offering features for
editing this view
• Open the Block Searcher web form and paste one of your protein sequences in
FASTA format
• Click ‘Perform Search’
• Save your result

Now we are going to use some of the ExPASy tools to perform a somewhat more
intensive sequence analysis. The idea is to use an unknown DNA sequence and find as
much as possible out about it with respect to our research area.

• Open the seq2.txt from the download page
• Use a translate tool to translate the sequence to all six reading frames
• Use these reading frames to query several databases of your choice (at least
InterPro Scan and MotifScan)
• Make use of several predictions programs (at least ChloroP, SignalP, PSORT and
TargetP)
• Finally, try to find out something about the physico-chemical parameters of the
protein sequences, the secondary structure (e.g. the helical content) and use a
modelling tool to predict the tertiary structure

Contact Jitendra Narayan