Question

I am writing a script in Perl which searches for a motif(substring) in protein sequence(string). The motif sequence to be searched (or substring) is hhhDDDssEExD, where:

• h is any hydrophobic amino acid
• s is any small amino acid
• x is any amino acid
• h,s,x can have more than one value separately

Can more than one value be assigned to one variable? If yes, how should I do that? I want to assign a list of multiple values to a variable.

Answer 1

I am no great expert in perl, so there is quite possibly a quicker way to this, but it seems like the match operator “//” in list context is what you need. When you assign the result of a match operation to a list, the match operator takes on list context and returns a list with each of the parenthesis delimited sub-expressions. If you specify global matches with the “g” flag, it will return a list of all the matches of each sub-expression. Example:

# print a list of each match for "x" in "xxx"
@aList = ("xxx" =~ /(x)/g);
print(join(".", @aList));

Will print out

x.x.x

I’m assuming you have a regular expression for each of those 5 types h, D, s, E, and x. You didn’t say whether each of these parts is a single character or multiple, so I’m going to assume they can be multiple characters. If so, your solution might be something like this:

$h = ""; # Insert regex to match "h"
$D = ""; # Insert regex to match "D"
$s = ""; # Insert regex to match "s"
$E = ""; # Insert regex to match "E"
$x = ""; # Insert regex to match "x"

$sequenceRE = "($h){3}($D){3}($s){2}($E){2}($x)($D)"

if ($line =~ /$sequenceRE/) {
    $hPart = $1;
    $sPart = $3;
    $xPart = $5;

    @hValues = ($hPart =~ /($h)/g);
    @sValues = ($sPart =~ /($s)/g);
    @xValues = ($xPart =~ /($x)/g);
}

I’m sure there is something I’ve missed, and there are some subtleties of perl that I have overlooked, but this should get you most of the way there. For more information, read up on perl’s match operator, and regular expressions.