[Bioperl-l] Thanks re Reverse Comp Coding Puzzler!

[David Nix]

Thanks guys!  Especially to Paul Boutros, Jamie Hatfield, and Shawn Hoon.
Your solutions work quite well.  If you're ever in Berkeley, do let me buy
you a beer.  -cheers, Dave

On 1/13/03 9:00 AM, "bioperl-l-request@bioperl.org"
<bioperl-l-request@bioperl.org> wrote:


> --__--__--
> 
> Message: 2
> Date: Mon, 13 Jan 2003 08:37:27 -0800
> From: David Nix <nix@uclink.berkeley.edu>
> To: <bioperl-l@bioperl.org>
> Subject: [Bioperl-l] Reverse Comp Coding Puzzler
> 
> Hello Folks,
>   I'm working on a perl program that identifies all restriction sites that
> can be inserted or deleted from an oligo used for site directed mutagenesis
> without changing the encoded amino acid sequence.  One problem that I need
> to overcome is how to get all unique oligo permutations of a 7 amino acid
> peptide, preferably one at a time.  These will be restriction mapped,
> compared to the original sequence one is mutating, and any differences
> ranked and returned to the user.
> 
> At first pass this seems like it should be easy, I can do it with pencil and
> paper, but getting it into a perl script is proving challenging for my
> novice programming skills.  Any suggestions or pointers you would have would
> be greatly appreciated!
> 
> Here's an example:
> 
> Take a peptide like...
> 
> M  P  V  A  R  D  I
> 
> Each amino acid is encoded by the following (I've got them in arrays)...
> my @M = qw(ATG);
> my @P = qw(CCA CCC CCG CCT);
> my @V = qw(GTA GTC GTG GTT);
> my @A = qw(GCA GCC GCG GCT);
> my @R = qw(CGA CGC CGG CGT AGA AGG);
> my @D = qw(GAC GAT);
> my @I = qw(ATA ATC ATT);
> 
> A few oligo permutation would be...
> $oligo1 = $M[0] . $P[0] . $V[0] . $A[0] . $R[0] . $D[0] . $I[0];
> $oligo2 = $M[0] . $P[0] . $V[0] . $A[0] . $R[0] . $D[0] . $I[1];
> $oligo3 = $M[0] . $P[0] . $V[0] . $A[0] . $R[0] . $D[0] . $I[2];
> 
> Now how would one write a script that gets at all the other 2301
> permutations (1 x 4 x 4 x 4 x 6 x 2 x 3)!  Ugg!  I've been at this for a day
> without much luck!  Suggestions?
> 
> Cheers, 
> Dave