Praedor Atrebates wrote:
> I am dinking around with perl for bioinformatics purposes. I have
> written a small perl script that reads FASTA formatted sequence files
> and searches the sequence therein for user-entered sequences.
>
> This is primarily targetted at protein sequence analysis and for my
> purposes, I've included - or am trying to include - one hard-coded
> sequence string.
>
> I have this (pertinent) code in my script:
>
> $dnakmotif = '[KRH][L{3,}V{3,}I{3,}F{3,}Y{3,}A{3,}][KRH];
>
$dnakmotif =
'[KPH](L{3,5}|V{3,5}|I{3,5}|F{3,5}|Y{3,5}|A{3,5}){1,}[KRH]';
This should allow some thing to start with KPH and have one or more of the
series of LVIFYA at least 3 and no more than 5 and ending with KRH.
Wags ;) ps not tested. A sample of data would hve been nice.
> print "Enter the motif/amino acid sequence pattern to search for:\n";
> $motif = <STDIN>;
> chomp $motif;
>
> if ($motif =~ 'dnak') {
> $motif = $dnakmotif;
> }
>
> Thus, if I enter the string "dnak" I want my query to be set to the
> value of $dnakmotif.
>
> I am just learning as I go here but there are two problems with this,
> one of which I understand but the other I do not. First, the one I
> do not understand. My intent with the value set to $dnakmotif was to
> search for K or R or H in a sequence followed by a string of 3 or
> more of any of the contents of the second bracket pair (L V I F Y A).
> When I run the program and run a search for "dnak" I get a string of
> hits in my test sequence they don't match what I am after. I get a
> series of hits, for instance, of a K followed by ONE A or ONE V
> followed by an H instead of at LEAST 3 of any of L or V or I, etc.
> Why doesn't this work?
>
> The next problem is one I understand but have no idea how to correct.
> The value I set to $dnakmotif is too restrictive for the actual
> searches I need to do. What I want is to search for a
> sequence/character string with any of K or R or H on either end, but
> _between them_ any combination of L, V, I, F, A, or Y is OK, in
> repeats or all individually so long as the minimum number is 3 and
> the max number (any combination of the characters) is _no more_ than
> 5. How do I make this character search be much less restrictive than
> I've started out with?
>
> Thank you for any aid,
> praedor
> --
> "Voice or no voice, the people can always be brought to the bidding of
> the leaders. That is easy. All you have to do is tell them they are
> being attacked, and denounce the peacemakers for lack of patriotism
> and exposing the country to danger. It works the same in any country."
> --Hermann Goering
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