Example 2: Finding first occurrence of start condon(ATG)

Overview

In this example, you will learn how to write a program that will find the position of the first occurrence of ATG in a sequence.

Example Code

Source Code

 

OutPut

The length of the sequence is 94

The position of first ATG occurrence is : 19

 

Decode

>>Line 13: $length= length($sequence);

length(STRING) is a perl function that will return the length of the STRING. In this case, length($sequence) returns the length of $sequence which is 94 and store this value into the variable $length.

>>Line 22: $firstOccurrence=index($sequence,"ATG",0)

index(STRING,SUBSTRING,POSITION) finds the SUBSTRING in a STRING and returns its index. POSITION indicates where to start looking for the SUBSTRING.

Note: The index of the first character in a String is 0, the second character 1, the third character 2, etc

In our case, index($sequence,"ATG",0) finds the first occurrence of "ATG" in $sequence starting from index 0. index($sequence,"ATG",44) will find the first occurrence of "ATG" in $sequence starting from index 44.

Note: index(STRING, SUBSTRING) will assume that POSITION is 0 . eg. index($seqeunce,"ATG") is the same as index($sequence,"ATG",0)

 

 

Exercise Two

>> Modify the above example to find the second occurrence of "ATG" in the sequence