1. Strings and Patterns in Perl Ellen Walker Bioinformatics Hiram College

2. Finding a Fixed Pattern my $string = “ATAAGCTTATCG”; my $pattern = “GCT”; print index($string,$pattern); print index (reverse($string), $pattern);

3. Finding multiple occurrences my $start = 0; print index($string, $pattern, $start); $start = index($string, $pattern, $start) + length($pattern); print index($string, $pattern, $start); $start = index($string, $pattern, $start) + length($pattern); When do you stop searching?

4. Finding all (non-overlapping) occurrences my $start = 0; my $found; $found = index($string, $pattern, $start); while ($found > -1) { print “$pattern found at $found\n”; $start = $found + length($pattern); $found = index($string, $pattern, $start); }

5. Pattern Matching Operators Three types of operators (so far) –Translation: tr –Substitution: s and g –Matching: m Used with =~ to modify a string Example: –$complement =~ tr/ACGT/TGCA/

6. Translation The tr operator takes two sequences of characters of the same length Every character in the first string is changed to the character at the same position in the second string This is destructive; save the old string before you use it!

7. Translation examples my $string = “actgTGCA”; my $capitalizedString = $string; $capitalizedString =~ tr/actg/ACTG/; my $lowerCaseString = $string; $lowerCaseString =~tr/ACTG/actg/;

8. Substitution Replaces an entire pattern with another pattern Patterns need not be the same length s changes only the first occurrence Add g to change all occurrences Example: –$string =~ s/T/U/g

9. Substitution Examples My $aminoAcids = $dna; $aminoAcids =~ s/AUG/Met/g; $aminoAcids =~ s/GGU/Gly/g; $aminoAcids =~ s/GGG/Gly/g; A sequence of these substitutions will not really work to translate RNA (why not?)

10. Matching Not destructive to the string Tests if the string matched (can be used as a condition in an if statement. Example: if ($string =~ m/T/) print “String is DNA, not RNA\n”;

11. Non-Exact Patterns Can be used with s or m Include – wildcard characters, –multiple option matches – capturing

12. Wildcard characters. Matches any character * Matches 0 or more characters equal to the preceding character + matches 1 or more… ^ before the beginning of the string $ matches after the end of the string

13. Multiple option matches [actg] Matches one character in the set a, c, t, g [^A-Z] Matches one character that is not A-Z TAG|TGA|TAA Matches either TAG, TGA or TAA –Example:my $Rpattern = ‘A|G’;

14. Capturing Patterns Any pattern in parentheses is “captured” The pattern can be recovered with \1, \2 etc. Example: s/(…)(…)/\2\1/ switches the first two codons in the string.

15. Slides are not Complete! Page 56-57 of the Perl book has an extensive list of regular expression examples.

16. Examples 6-mer palindrome (.)(.)(.)\3\2\1 Pair of nucleotides repeated at least three times (.)(.).*\1\2.*\1\2 Strings that end with GGA GGA$