This practical has been sligthly edited and heavily mutilated by Roderic Guigó (IMIM and UPF), to be used with the internet version of clustalw at the ebi, instead of Clustal X. Credit is for the authors below. The original practical is here.

• Sequence extraction and alignment tools.
• Exercise 1: Extracting and aligning NusA sequences..

Sequence Extraction and Alignment Tools

We will use:

• SRS (at EBI or EMBL) to extract and save a group of sequences to align.
• Clustal W (at EBI)

Exercise 1: Extracting and Aligning NusA Sequences.

NusA is an RNA-binding transcriptional regulatory protein within the RNA Polymerase complex of E. coli and other prokaryotes, including the Archaea. It influences whether to terminate or read-through termination control sites in operons.


Extracting NusA Sequences:

• Load SRS (at EBI or EMBL) and Start the session.
• Select the Swiss-Prot database and continue.
• Type nusa in the ID box, then Do Query.
• Click the save button.
• Select FastaSeqs view and fasta sequence format. Click on the save button
• Open Netscape Save As menu (in File).
• Set to Text format, and save as e.g. nusa.dat.

• Load Clustal W at at EBI
• Familiarise yourself with the layout and menus.
• With Upload a file read in the Nusa set.
• Now RUN CLUSTAL W
• Wait for the analysis to finish
• Scroll dwon to review the alignment.
• Use JalView for a Java interface to the alignment