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Step by Step Instructions for running PILEUP

In order to align a group of sequences with PILEUP, it is first necessary to create a list of the names of sequences to be aligned in GCG's .LIST file format.

The output of the GCG LOOKUP program is a .LIST file.

Output from FASTA searches can also be used as a .LIST file.

You can also create your own .LIST with the VMS text editor EVE (or EDT).

• Give these list files names that end with the .LIST extension.
  
  
• Sequence names are typed in one per line.
  
  
• Either database names (i.e. gb_ro:ratnrdc) or the names of files in your working directory can be used (i.e. myseq.pep ), or a mixture of these.
  
  
• Add a first line to the file of names that just has two period characters (..).

The final list file should look like this:

$ type ide.list

    ..
    gp:S31321           
    gp:Yno3_Yeast     
    S51900           
    Yan2_Schpo       
    Ypd1_Caeel     
    A36205          
    Mpp1_Rat      
    B46665       
    Ymxg_Bacsu     
    A48043

Now at the $ prompt, type PILEUP and the name of the file that is your list of sequence names

However - and this is extremely silly - you must precede the name of your list file with the @ character.

So the command looks like this:

$ PILEUP @myseqs.list 

I recommend that you use the default settings that PILEUP offers, but you can certainly change the name of the output file.

If you are aligning more than about 10 sequences, PILEUP is going take quite a while, so it would be a good idea to run it in batch mode:

$ PILEUP/bat @myseqs.list 

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Using Computers for Molecular Biology
Stuart M. Brown, Ph.D., RCR, NYU Medical Center

Comments to: browns02@mcrcr.med.nyu.edu