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3475. DNA Pattern Recognition

Description

Table: Samples

+----------------+---------+
| Column Name    | Type    | 
+----------------+---------+
| sample_id      | int     |
| dna_sequence   | varchar |
| species        | varchar |
+----------------+---------+
sample_id is the unique key for this table.
Each row contains a DNA sequence represented as a string of characters (A, T, G, C) and the species it was collected from.

Biologists are studying basic patterns in DNA sequences. Write a solution to identify sample_id with the following patterns:

  • Sequences that start with ATG (a common start codon)
  • Sequences that end with either TAA, TAG, or TGA (stop codons)
  • Sequences containing the motif ATAT (a simple repeated pattern)
  • Sequences that have at least 3 consecutive G (like GGG or GGGG)

Return the result table ordered by sample_id in ascending order.

The result format is in the following example.

 

Example:

Input:

Samples table:

+-----------+------------------+-----------+
| sample_id | dna_sequence     | species   |
+-----------+------------------+-----------+
| 1         | ATGCTAGCTAGCTAA  | Human     |
| 2         | GGGTCAATCATC     | Human     |
| 3         | ATATATCGTAGCTA   | Human     |
| 4         | ATGGGGTCATCATAA  | Mouse     |
| 5         | TCAGTCAGTCAG     | Mouse     |
| 6         | ATATCGCGCTAG     | Zebrafish |
| 7         | CGTATGCGTCGTA    | Zebrafish |
+-----------+------------------+-----------+

Output:

+-----------+------------------+-------------+-------------+------------+------------+------------+
| sample_id | dna_sequence     | species     | has_start   | has_stop   | has_atat   | has_ggg    |
+-----------+------------------+-------------+-------------+------------+------------+------------+
| 1         | ATGCTAGCTAGCTAA  | Human       | 1           | 1          | 0          | 0          |
| 2         | GGGTCAATCATC     | Human       | 0           | 0          | 0          | 1          |
| 3         | ATATATCGTAGCTA   | Human       | 0           | 0          | 1          | 0          |
| 4         | ATGGGGTCATCATAA  | Mouse       | 1           | 1          | 0          | 1          |
| 5         | TCAGTCAGTCAG     | Mouse       | 0           | 0          | 0          | 0          |
| 6         | ATATCGCGCTAG     | Zebrafish   | 0           | 1          | 1          | 0          |
| 7         | CGTATGCGTCGTA    | Zebrafish   | 0           | 0          | 0          | 0          |
+-----------+------------------+-------------+-------------+------------+------------+------------+

Explanation:

  • Sample 1 (ATGCTAGCTAGCTAA):
    • Starts with ATG (has_start = 1)
    • Ends with TAA (has_stop = 1)
    • Does not contain ATAT (has_atat = 0)
    • Does not contain at least 3 consecutive 'G's (has_ggg = 0)
  • Sample 2 (GGGTCAATCATC):
    • Does not start with ATG (has_start = 0)
    • Does not end with TAA, TAG, or TGA (has_stop = 0)
    • Does not contain ATAT (has_atat = 0)
    • Contains GGG (has_ggg = 1)
  • Sample 3 (ATATATCGTAGCTA):
    • Does not start with ATG (has_start = 0)
    • Does not end with TAA, TAG, or TGA (has_stop = 0)
    • Contains ATAT (has_atat = 1)
    • Does not contain at least 3 consecutive 'G's (has_ggg = 0)
  • Sample 4 (ATGGGGTCATCATAA):
    • Starts with ATG (has_start = 1)
    • Ends with TAA (has_stop = 1)
    • Does not contain ATAT (has_atat = 0)
    • Contains GGGG (has_ggg = 1)
  • Sample 5 (TCAGTCAGTCAG):
    • Does not match any patterns (all fields = 0)
  • Sample 6 (ATATCGCGCTAG):
    • Does not start with ATG (has_start = 0)
    • Ends with TAG (has_stop = 1)
    • Starts with ATAT (has_atat = 1)
    • Does not contain at least 3 consecutive 'G's (has_ggg = 0)
  • Sample 7 (CGTATGCGTCGTA):
    • Does not start with ATG (has_start = 0)
    • Does not end with TAA, "TAG", or "TGA" (has_stop = 0)
    • Does not contain ATAT (has_atat = 0)
    • Does not contain at least 3 consecutive 'G's (has_ggg = 0)

Note:

  • The result is ordered by sample_id in ascending order
  • For each pattern, 1 indicates the pattern is present and 0 indicates it is not present

Solutions

Solution 1: Fuzzy Matching + Regular Expressions

We can use LIKE and REGEXP for pattern matching, where:

  • LIKE 'ATG%' checks if it starts with ATG
  • REGEXP 'TAA$|TAG$|TGA$' checks if it ends with TAA, TAG, or TGA ($ indicates the end of the string)
  • LIKE '%ATAT%' checks if it contains ATAT
  • REGEXP 'GGG+' checks if it contains at least 3 consecutive Gs
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# Write your MySQL query statement below
SELECT
    sample_id,
    dna_sequence,
    species,
    dna_sequence LIKE 'ATG%' AS has_start,
    dna_sequence REGEXP 'TAA$|TAG$|TGA$' AS has_stop,
    dna_sequence LIKE '%ATAT%' AS has_atat,
    dna_sequence REGEXP 'GGG+' AS has_ggg
FROM Samples
ORDER BY 1;

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import pandas as pd


def analyze_dna_patterns(samples: pd.DataFrame) -> pd.DataFrame:
    samples["has_start"] = samples["dna_sequence"].str.startswith("ATG").astype(int)
    samples["has_stop"] = (
        samples["dna_sequence"].str.endswith(("TAA", "TAG", "TGA")).astype(int)
    )
    samples["has_atat"] = samples["dna_sequence"].str.contains("ATAT").astype(int)
    samples["has_ggg"] = samples["dna_sequence"].str.contains("GGG+").astype(int)
    return samples.sort_values(by="sample_id").reset_index(drop=True)

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