APT, Promotion and tata boxes I

Problem Statement

Transcription for protein-coding regions is often indicated by a TATA box, a sequence of nucleotides TATAA just prior to the actual encoding region. Locating a TATA box is what RNA "does" in finding proteins and what you will do in this problem.

In this problem you'll analyze only part of a DNA sequence in looking for TATA boxes. In real genomic data a TATA box that indicates a possible protein coding sequence must be followed by a start codon ATG located approximately 150 base pairs from the TATA box. In this program rather than 150 you'll use the range (20-30).

Any DNA sequence with a TATA-box located 20-30 base-pairs before a start codon is a possible protein source. The distance between the last A in TATAA and the first A in ATG must be 20-30 nucleotides in this problem. You may need to find more than one TATA box, see the examples for details. Any TATA box with a start codon 20-30 nucleotides away is a predictor for gene/protein finding.

Given a DNA sequence string, return the index/location of the start of the first TATA box that predicts a protein coding region (start codon 20-30 nucleotides from the end of the box). Return -1 if there is no protein-predicting TATA box.

Definition

Class: TATAProteinFinder
Method: tata
Parameters: String
Returns: int
Method signature:
```
  public int tata(String dna)
```
(be sure your method is public)

Class
public class TATAProteinFinder { public int tata(String dna) { // fill in code here } };
Notes
The range (20,30) between the end of the TATA box and the beginning of the start codon is the number of nucleotides between the last A of the TATA box and the first A of the start codon, not including these A nucleotides.
Constraints
- Each String will have a length of less than 200.
- All characters of the strings will be in upper case letters from 'A', 'T', 'C', and 'G'
Examples
1. ```
"TATAAGGGGGGGGGGGGGGGGGGGGGGGGGATGCC"

return 0
```
  The TATA box at the beginning of the string is followed by a start codon after 25 nucleotides.
2. ```
"TATAAGGGGGGGGGGGGGGGGGGGATGCC"

return -1
```
  The start codon is 19 nucleotides from the start, this isn't between 20 and 30 so return -1.
3. ```
"TATAAGGGGGGGGGGGGGGGGGGGGGGGGGATCC"

return -1
```
  There is no start codon
4. ```
"ATGATGATGTATAAGGGGGGGGGGGGGGGGGGGGGGGGGATGCC"

return 9
```
  like the first example with some extra nucleotides before the TATA box.
5. ```
"TATAAGGGGGGGGGGAGTGGGTATAACCCCCCCCCCCCCCCCCCCCCCAGTCCC"

return 21
```
  The first TATA box is 10 away from a start codon, but the second TATA box, starting at index 21 is 22 nucleotides away from a start codon, so return 21.
Owen L. Astrachan
Last modified: Thu Nov 8 10:12:23 EST 2007

APT, Promotion and tata boxes I

Problem Statement

Definition

Class

Notes

Constraints

Examples