• Skip this description and get to the example.

    clustalw: To align a group of Protein Sequences in table format.

      The clustalw program is an easy to use menu-driven program that accepts various file formats. This software was described in: Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, submitted, June 1994. Be sure to convert your IG formatted sequence file to Fasta format. (You can use readseq to do this). Then type clustalw to run the program. This program is very user-friendly and has online help. For more information, see the readme.txt and clustalw.ms files in the directory /usr/local/src/clustalw 
      

      The following is a short tutorial on how to align a group of
sequences with the clustalw program.

      



      cyrus% gcg <Return>

      


      First, Fetch a sequence to use as a query sequence. The GCG
program called "fetch" will fetch a sequence from your local
database.  The sequence will be saved in a file with the name of
the database appended at the end of the name.  For example, the
sequence "hba_human" is saved in a file called "hba_human.swissprot"
because "hba_human" comes from the Swissprot database.
      

      cyrus% fetch hba_human <Return>

      

      Now, do the same for the rest of your sequences. 
      

cyrus%  toig *.swissprot <Return>

  ToIG converts GCG sequence file(s) into a single file in
  IntelliGenetics format.

   glb5petma 149 aa
   hbahorse 141 aa
   hbahuman 141 aa
   hbbhorse 146 aa
   hbbhuman 146 aa
   lgb2luplu 153 aa
   mygphyca 153 aa

   What should I call the output file (* glb5_petma.ig *) ?  hb.ig
  

  Note:  Now put all of the IG sequences into one file and convert
  it to fasta format with the readseq program.

cyrus% dir *.ig <Return>
   2 1coh.ig       2 2mhb.ig     136 hb.ig
cyrus% cat 1coh.ig 2mhb.ig hb.ig > temp.ig <Return>

cyrus% readseq<Return>
Enter an output filename:
hb.fa<Return>
Choose an output format (name or #): 
8<Return>
Name an input sequence or -option:
temp.ig<Return>
Choose a sequence (# or All): 
all <Return>
Name an input sequence or -option:
Hit Return key<Return>

cyrus% more hb.fa

cyrus% clustalw  <Return>
    In the main menu, enter
    1. Sequence Input From Disc
Your choice: 1
    You will be asked for your sequence file which can be in
    any of the following formts:
    NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF
Enter the name of the sequence file: horse.fa
    You will return to the main menu.  Now enter the choice for 
    2. Multiple Alignments
Your choice: 2
    In the ****** MULTIPLE ALIGNMENT MENU ****** enter
    9.  Output format options
Your choice: 9
    3. Toggle GCG/MSF format output     =  OFF
Enter number (or [RETURN] to exit): 3
Enter number (or [RETURN] to exit): 4

At the "****** MULTIPLE ALIGNMENT MENU ******"
    1.  Do complete multiple alignment now (Slow/Accurate)

Your choice: 1
Enter a name for the CLUSTAL output file  [horse.aln]:
Enter a name for the GCG output file      [horse.msf]: 
Enter a name for the PHYLIP output file   [horse.phy]: 
Enter name for GUIDE TREE          file   [horse.dnd]: 
Press [RETURN] to continue or  X  to stop: 
Press [RETURN] to continue or  X  to stop: 
Press [RETURN] to continue: 
Your choice: 


     4. Phylogenetic trees
Your choice: 4

    2.  Exclude positions with gaps?        = OFF
    3.  Correct for multiple substitutions? = OFF
Your choice: 2
Your choice: 3
    4.  Draw tree now
Your choice: 4
Enter name for PHYLIP     tree output file   [horse.ph]:

To print out the tree, use the phylip program drawtree or drawgram

cyrus%  drawtree<Return>
drawtree:  can't read fontfile
Please enter a new filename> /opt/pkg/PHYLIP/font1<Return>
              printer?        (Select choice L--Apple Laserwriter)
                preview? N
        (drawtree will create a postscript file called    plotfile)
        ghostview plotfile              (To look at tree on screen--make
                                         sure your DISPLAY variable is set.)
        lpr -Plw plotfile               (To print out plotfile.)


      The clustalw program will create the following output files. 
      
cyrus% dir horse*  <Return>
-rw-r--r--   1 tom      users        397 Sep  3 15:45 horse.ph
-rw-r--r--   1 tom      users       3739 Sep  3 15:42 horse.msf
-rw-r--r--   1 tom      users       2276 Sep  3 15:42 horse.phy
-rw-r--r--   1 tom      users        397 Sep  3 15:41 horse.dnd
-rw-r--r--   1 tom      users       3200 Sep  3 15:37 horse.aln
cyrus%

      


      You can align your sequences with clustalw at
our WWW site athttp://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/


      You can access a comprehensive list of multiple alignment
programs at the VSNS BioComputing Division Multiple Alignment Resource Page
http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html


      You can learn more about multiple sequence alignments by going to
the ALGORITHMS FOR MULTIPLE SEQUENCE ALIGNMENTS homepage at the www site
http://ben.vub.ac.be/embnet.news/vol2_1/align.html