[Bioperl-l] Clustal w - fixed width characters

Tariq Shafi tariq_shafi75 at hotmail.com
Thu Jun 17 15:48:16 EDT 2004


I am using a Clustalw alignment and in doing the alignment I want to format 
my alignment results in fixed width characters.

I get an object called $alignment from the Clustalw operation, using 

Later on, I am using the following code:

foreach $seq ($alignment->each_seq) {
    print b($seq->id(), ':');
    $str = $seq->seq();
    print $str, br();

This gives alignments but they are difficult to visualise as the characters 
are not of fixed width, so (visually only) it is out of sync. How do I make 
the characters in each sequence of fixed width?



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