Student practical for Sequence Alignment, Oct. 1996

Sequence Analysis Group
(Room V325, ext. 398)

In this practical you shall learn how to extract a list of sequences from different databases and how to align them with ClustalW.

Computational steps to perform

Open Netscape to link with WWW.

Search with keywords, IDs, Accession numbers (depending on what is available) the estrogen receptors in the databases. Use SRS (EBI) or SRS (EMBL) and search e.g. in SwissProt and PIR. To exclude keywords (e.g. fragment) use the querymanager.

When you have got your final sequence list, save it as a file (file -> save as ..) and edit this file with an editor (e.g. nedit). At the end the file should have the following format: 

database:sequencename
database:sequencename
e.g.
SW:ESTR_CHICK
SWISSNEW:ESTR_BOVIN

Fetch the sequences into wpie:

  1. Prepare GCG and open wpie.
  2. Load the sequences. Under database specification enter: @directory/filename.
  3. Select all the sequences in the file (double-click on the filename and mark them all).
  4. Save the sequence file into PIR format using ToPIR.
  5. The PIR output file (see Output Manager) can be used as input for ClustalW.

Alignment:

  1. Prepare ClustalW (command: prepare clustalw)
  2. Start ClustalW (command: clustalw)
  3. Use option 1 (1. Sequence Input From Disc) to get the sequences into ClustalW. (Give the name of your PIR format file).
  4. Option 2 (2. Multiple Alignments) leads you to the alignment menue.
  5. Option 1 (1. Do complete multiple alignment now (Slow/Accurate)) performs the alignment.

Print the alignment:

Print the alignment file .aln with the command lpr -Plw-v327 file.aln

Optional: display the alignment and the tree with Phylowin:

  1. Prepare Phylowin (command: prepare phylowin)
  2. Start Phylowin (command: phylowin)
  3. Load alignment file (with extension .aln)
  4. Click input tree and load dnd file.
  5. Click the loaded filename and draw tree.
ClustalW is available on VMS/Unix machines. After preparing it the some documentation is available at $Clustalw_Dir/Clustalv.doc. You can read it with e.g. the command 'less $Clustalw_Dir/Clustalv.doc'.

(GCG is available on VMS/Unix machine. you have to 'prepare' before using it. e.g. prepare gcg command).
There is a new graphical interface for this on unix. Type wpie to access it.

http address of this page
http://www.embl-heidelberg.de/~seqanal/courses/align_oct96.html