Difference between revisions of "KSH 0608 Bioinformatics with Bioperl"

Revision as of 23:57, 8 June 2016

From today, I will learn and summarize how to use Bioperl by reading a book "Bioinformatics with bioperl (Author: Young-Chang Kim)"

1. Change DNA sequence to RNA sequence

$DNASeq = 'GATACAA.......'

$RNASeq =~s/T/U/g;

=~ : binding operator tells Perl to match the pattern on the right against the string on the left

s/ / / : substitution function, s is substitution operator, / is used to make a distinction

g : pattern modifier from start to end

==> We can utilize the =~s/ / /g to the first homework

If there is a certain DNA sequence, we can change the sequence into matching amino acid sequence

For example, Methionine has AUG codon sequence and its template DNA sequence is 3'-TAC-5'.

Thus, if we change the CAT sequence into M or Met, we could find the methionine from DNA sequence.

Ex) $Methionine = ~s/CAT/M/g;

Likewise, we could derive whole amino acids from DNA sequence.