From d4ea63bdeb5a9cd3dfcb0f25adf6acdf2636dc4b Mon Sep 17 00:00:00 2001 From: enzo Date: Wed, 12 Mar 2025 15:49:47 +0100 Subject: [PATCH] p --- BINF2025_TP3.ipynb | 1092 +++++++++++++++++++++++++------------------- 1 file changed, 620 insertions(+), 472 deletions(-) diff --git a/BINF2025_TP3.ipynb b/BINF2025_TP3.ipynb index 61e87c2..f8cf678 100644 --- a/BINF2025_TP3.ipynb +++ b/BINF2025_TP3.ipynb @@ -1,481 +1,629 @@ { - "nbformat": 4, - "nbformat_minor": 0, - "metadata": { + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "id": "V09wQ1WIOmgn" + }, + "source": [ + "# BINF TP3 - Algorithmes d'alignement par paire" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "er6CtAyOxC6F" + }, + "source": [ + "Dans ce TP nous allons manipuler les algorithmes d'alignement par paire." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "BqEa3BJ1xICM" + }, + "source": [ + "# Exercice 0 - Echauffement" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "qqiiq5bcxYvM" + }, + "source": [ + "Q1. Donnez le score de la superposition :\n", + "\n", + "| | |\n", + "| :---: | :---: |\n", + "x | ATGTCATGA---TAC |\n", + "y | AT--CTAAATGTTAC |\n", + "\n", + "\n", + "étant donne le schéma d'évaluation :\n", + "\n", + "| | A | T | G | C |\n", + "| :---: | :---: | :---: | :---: | :---: |\n", + "| **A** | 1 | -1 | -1 | -1 |\n", + "| **T** | -1 | 1 | -1 | -1 |\n", + "| **G** | -1 | -1 | 1 | -1 |\n", + "| **C** | -1 | -1 | -1 | 1 |\n", + "\n", + "et\n", + "\n", + "$\\gamma(g) = 0.5 |g| + 0.5$" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "kCJGGGYQ2GNi" + }, + "source": [ + "```markdown\n", + "1+1+1-1-1-1+1+1+1+1 = 4\n", + "2 gap = 1.5 + 2 = 3.5\n", + "result = 4-3.5 = 0.5\n", + "```" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "XyhXAhK-2NKJ" + }, + "source": [ + "Q2. Alignez les séquences suivantes avec l'algorithme de Levenshtein : x = ATG et y = ACTG." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "b9iovhyZ2bXw" + }, + "source": [ + "```markdown\n", + "ATG | ACTG -> 0\n", + "\n", + "TG | CTG -> 1 + min (G|TG, TG|TG, G|CTG) -> TG|TG = 0\n", + "\n", + "result = A_TG|ACTG score = 1\n", + "```" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "OV_YaQHr2elB" + }, + "source": [ + "Q3.\tAlignez les séquences suivantes avec l'algorithme de Needleman-Wunsch global x = TAT et y = ATGAC en considérant le schéma d'évaluation suivant\n", + "\n", + "| | A | T | G | C |\n", + "| :---: | :---: | :---: | :---: | :---: |\n", + "| **A** | 1 | -0.5 | -0.5 | -0.5 |\n", + "| **T** | -0.5 | 1 | -0.5 | -0.5 |\n", + "| **G** | -0.5 | -0.5 | 1 | -0.5 |\n", + "| **C** | -0.5 | -0.5 | -0.5 | 1 |\n", + "\n", + "et\n", + "\n", + "$\\gamma(g) = 0.5 |g|$\n", + "\n", + "ATGAC\n", + "_T_AT " + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "g_MrecVs3Nrw" + }, + "source": [ + "S: \n", + "| | V | A | T | G | A | C |\n", + "| :---: | :---: | :---: | :---: | :---: | :---: | :---: |\n", + "| **V** | 0 | -0.5 | -1 | -1.5 | -2 | -2.5 |\n", + "| **T** | -0.5 | -0.5 | 0.5 | 0 | -0.5 | -1 |\n", + "| **A** | -1 | 0.5 | 0 | 0 | 1 | 0.5 |\n", + "| **T** | -1.5 | 0 | 1.5 | 1 | 0.5 | 0.5 |\n", + "\n", + "B:\n", + "\n", + "\n", + "| | V | A | T | G | A | C |\n", + "| :---: | :---: | :---: | :---: | :---: | :---: | :---: |\n", + "| **V** | F | G | G | G | G | G |\n", + "| **T** | M | DIA | DIA | G | G | G |\n", + "| **A** | M | DIA | G | DIA | DIA | G |\n", + "| **T** | M | M | DIA | G | G | DIA |\n", + "\n" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "y1YF-G6E3Qoo" + }, + "source": [ + "Q4. Alignez les séquences suivantes avec l'algorithme de Smith-Waterman x = TTGG y = ATGAC en utilisant le schéma d'évaluation de la question précédente.\n" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "LLMECocb3pgI" + }, + "source": [ + "```markdown\n", + "Votre réponse ici\n", + "```" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "46gw0avh3wGw" + }, + "source": [ + "# Exercice 1 : Algorithme de Levenshtein - version récursive" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "ZKc09Kyg4a6v" + }, + "source": [ + "Q1. Ecrivez une fonction\n", + "\n", + "levenshtein(x: str, y: str) -> int\n", + "\n", + "qui retourne la distance de Levenshtein entre les séquences x et y en utilisant la version récursive de l'algorithme." + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "id": "FJR69IEQ4aHv" + }, + "outputs": [], + "source": [ + "def levenshtein(x,y):\n", + " if len(x) == 0:\n", + " return len(y)\n", + " elif len(y) == 0:\n", + " return len(x)\n", + " elif x[0] == y[0]:\n", + " return levenshtein(x[1:],y[1:])\n", + " else:\n", + " return 1 + min(levenshtein(x[1:],y[1:]),levenshtein(x[1:],y),levenshtein(x,y[1:]))" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "arFVwA6E5NWn" + }, + "source": [ + "Q2. Vous pouvez tester votre code sur les exemples suivants:\n", + "\n", + "\n", + "* $L('CCAG', 'CA') = 2$\n", + "* $L('CCGT', 'CGTCA') = 3$\n", + "* $L(AY678264^*, OQ870305^*) = 310$\n", + "\n", + "$^*$ ids genbank de deux sequences." + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2\n", + "3\n", + "7\n" + ] + } + ], + "source": [ + "print(levenshtein(\"CCAG\", \"CA\"))\n", + "print(levenshtein(\"CCGT\", \"CGTCA\"))\n", + "print(levenshtein(\"AY678264\", \"OQ870305\"))" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "erCpfG7O7BV-" + }, + "source": [ + "# Exercice 2 : Algorithme de Smith-Waterman - version itérative" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "rv2Y78y37IOd" + }, + "source": [ + "Q1. Ecrivez la fonction\n", + "\n", + "sw_fwd(x: str, y: str, cmap: dict, sigma: array, (go, ge): list) -> (array, array)\n", + "\n", + "qui construit les matrices $S$ et $B$ en utilisant l'algorithme de Smith-Waterman pour aligner les séquences x et y suivant le schéma d'évaluation donné par la matrice de substitution $\\Sigma$ et la fonction d'évaluation des trous $\\gamma(n)= g_o + g_e \\times n$. Le dictionnaire cmap donne la position des différents nucléotides dans la matrice $\\Sigma$. La fonction retourne la paire de matrices de score $S$ et de retour $B$." + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": { + "id": "njn3JB0b-WHj" + }, + "outputs": [], + "source": [ + "def sw_fwd(x,y,cmap,sigma,go,ge):\n", + " S = [[0 for _ in range(len(y) + 1)] for _ in range(len(x) + 1)]\n", + " B = [[(0,0) for _ in range(len(y) + 1)] for _ in range(len(x) + 1)]\n", + " \n", + " for i in range(1,len(x) + 1):\n", + " for j in range(1,len(y) + 1):\n", + " a = sigma[cmap[x[i-1]]][cmap[y[j-1]]] + S[i-1][j-1]\n", + " b = S[i][j-1] - (go + ge)\n", + " c = S[i-1][j] - (go + ge)\n", + " n = max(a,b,c,0)\n", + " S[i][j] = n\n", + "\n", + " if n == 0:\n", + " B[i][j] = (0,0)\n", + " elif n == a:\n", + " B[i][j] = (-1,-1)\n", + " elif n == b:\n", + " B[i][j] = (0,-1)\n", + " elif n == c:\n", + " B[i][j] = (-1,0)\n", + " else:\n", + " B[i][j] = (0,0)\n", + " return S,B" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "55n8mt9U-Wai" + }, + "source": [ + "Q2. Ecrivez la fonction\n", + "\n", + "sw_bwd(x: str, y: str, S: array, B: array) -> (str, str, float)\n", + "\n", + "qui effectue l'etape de retour de l'algorithme de Smith-Waterman etant donné les séquences $x$ et $y$ et les matrices de score $S$ et de retour $B$. La fonction retourne un tuple contenant les alignements des séquences x et y et le score de l'alignement." + ] + }, + { + "cell_type": "code", + "execution_count": 49, + "metadata": { + "id": "ij9JDpBm_UZ7" + }, + "outputs": [], + "source": [ + "def find_max(matrix):\n", + " max_value = float('-inf') \n", + " max_indices = (-1, -1) \n", + "\n", + " for i in range(len(matrix)):\n", + " for j in range(len(matrix[i])): \n", + " if matrix[i][j] > max_value:\n", + " max_value = matrix[i][j]\n", + " max_indices = (i, j) \n", + "\n", + " return max_value, max_indices\n", + "\n", + "def sw_bwd(x,y,S,B):\n", + " score, (i,j) = find_max(S)\n", + " result_X = \"\"\n", + " result_Y = \"\"\n", + " Ni,Nj = B[i][j]\n", + " while (Ni,Nj) != (0,0):\n", + " if (Ni == -1):\n", + " result_X = x[i-1] + result_X\n", + " i = i-1\n", + " else:\n", + " result_X = \"_\" + result_X\n", + " if (Nj == -1):\n", + " result_Y = y[j-1] + result_Y\n", + " j = j-1\n", + " else:\n", + " result_Y = \"_\" + result_Y\n", + " Ni,Nj = B[i][j]\n", + " return (result_X, result_Y, score)" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "kwmxg2dxAiwS" + }, + "source": [ + "Q3. Vous pouvez tester votre code en utilisant le schéma d'évaluation suivant :" + ] + }, + { + "cell_type": "code", + "execution_count": 52, + "metadata": { + "id": "JUtYRFTBAwwZ" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "('TCG', 'TAG', 1.5)\n" + ] + } + ], + "source": [ + "cmap = {\"A\": 0, \"T\": 1, \"G\": 2, \"C\": 3}\n", + "m = [[1, -0.5, -0.5, -0.5],\n", + " [-0.5, 1, -0.5, -0.5],\n", + " [-0.5, -0.5, 1, -0.5],\n", + " [-0.5, -0.5, -0.5, 1]]\n", + "go = 0\n", + "ge = 0.5\n", + "\n", + "S,B = sw_fwd(\"TCGC\", \"CTTAG\", cmap, m, go, ge)\n", + "\n", + "print(sw_bwd(\"TCGC\", \"CTTAG\", S, B))" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "eMGh4K5aIFxE" + }, + "source": [ + "* $SW('TCGC', 'CTTAG')$ retourne un score de $1.5$ à la position $(3,5)$ et l'alignement" + ] + }, + { + "cell_type": "code", + "execution_count": 53, + "metadata": { "colab": { - "provenance": [], - "authorship_tag": "ABX9TyNSXnqaXAUgZK9rmJ1TWbGo" - }, - "kernelspec": { - "name": "python3", - "display_name": "Python 3" - }, - "language_info": { - "name": "python" + "base_uri": "https://localhost:8080/", + "height": 60 + }, + "id": "joHNwJ9AIf6F", + "outputId": "a9206810-a083-4d86-8b14-38183f1dd80c" + }, + "outputs": [ + { + "ename": "NameError", + "evalue": "name 'HTML' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m/tmp/ipykernel_7301/646597341.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mHTML\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"
x:TCG
y:TAG
\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mNameError\u001b[0m: name 'HTML' is not defined" + ] } + ], + "source": [ + "HTML(\"
x:TCG
y:TAG
\")" + ] }, - "cells": [ - { - "cell_type": "markdown", - "source": [ - "# BINF TP3 - Algorithmes d'alignement par paire" - ], - "metadata": { - "id": "V09wQ1WIOmgn" - } - }, - { - "cell_type": "markdown", - "source": [ - "Dans ce TP nous allons manipuler les algorithmes d'alignement par paire." - ], - "metadata": { - "id": "er6CtAyOxC6F" - } - }, - { - "cell_type": "markdown", - "source": [ - "# Exercice 0 - Echauffement" - ], - "metadata": { - "id": "BqEa3BJ1xICM" - } - }, - { - "cell_type": "markdown", - "source": [ - "Q1. Donnez le score de la superposition :\n", - "\n", - "| | |\n", - "| :---: | :---: |\n", - "x | ATGTCATGA---TAC |\n", - "y | AT--CTAAATGTTAC |\n", - "\n", - "\n", - "étant donne le schéma d'évaluation :\n", - "\n", - "| | A | T | G | C |\n", - "| :---: | :---: | :---: | :---: | :---: |\n", - "| **A** | 1 | -1 | -1 | -1 |\n", - "| **T** | -1 | 1 | -1 | -1 |\n", - "| **G** | -1 | -1 | 1 | -1 |\n", - "| **C** | -1 | -1 | -1 | 1 |\n", - "\n", - "et\n", - "\n", - "$\\gamma(g) = 0.5 |g| + 0.5$" - ], - "metadata": { - "id": "qqiiq5bcxYvM" - } - }, - { - "cell_type": "markdown", - "source": [ - "```markdown\n", - "Votre réponse ici\n", - "```" - ], - "metadata": { - "id": "kCJGGGYQ2GNi" - } - }, - { - "cell_type": "markdown", - "source": [ - "Q2. Alignez les séquences suivantes avec l'algorithme de Levenshtein : x = ATG et y = ACTG." - ], - "metadata": { - "id": "XyhXAhK-2NKJ" - } - }, - { - "cell_type": "markdown", - "source": [ - "```markdown\n", - "Votre réponse ici\n", - "```" - ], - "metadata": { - "id": "b9iovhyZ2bXw" - } - }, - { - "cell_type": "markdown", - "source": [ - "Q3.\tAlignez les séquences suivantes avec l'algorithme de Needleman-Wunsch global x = TAT et y = ATGAC en considérant le schéma d'évaluation suivant\n", - "\n", - "| | A | T | G | C |\n", - "| :---: | :---: | :---: | :---: | :---: |\n", - "| **A** | 1 | -0.5 | -0.5 | -0.5 |\n", - "| **T** | -0.5 | 1 | -0.5 | -0.5 |\n", - "| **G** | -0.5 | -0.5 | 1 | -0.5 |\n", - "| **C** | -0.5 | -0.5 | -0.5 | 1 |\n", - "\n", - "et\n", - "\n", - "$\\gamma(g) = 0.5 |g|$\n" - ], - "metadata": { - "id": "OV_YaQHr2elB" - } - }, - { - "cell_type": "markdown", - "source": [ - "```markdown\n", - "Votre réponse ici\n", - "```" - ], - "metadata": { - "id": "g_MrecVs3Nrw" - } - }, - { - "cell_type": "markdown", - "source": [ - "Q4. Alignez les séquences suivantes avec l'algorithme de Smith-Waterman x = TTGG y = ATGAC en utilisant le schéma d'évaluation de la question précédente.\n" - ], - "metadata": { - "id": "y1YF-G6E3Qoo" - } - }, - { - "cell_type": "markdown", - "source": [ - "```markdown\n", - "Votre réponse ici\n", - "```" - ], - "metadata": { - "id": "LLMECocb3pgI" - } - }, - { - "cell_type": "markdown", - "source": [ - "# Exercice 1 : Algorithme de Levenshtein - version récursive" - ], - "metadata": { - "id": "46gw0avh3wGw" - } - }, - { - "cell_type": "markdown", - "source": [ - "Q1. Ecrivez une fonction\n", - "\n", - "levenshtein(x: str, y: str) -> int\n", - "\n", - "qui retourne la distance de Levenshtein entre les séquences x et y en utilisant la version récursive de l'algorithme." - ], - "metadata": { - "id": "ZKc09Kyg4a6v" - } - }, - { - "cell_type": "code", - "source": [ - "#Votre code ici" - ], - "metadata": { - "id": "FJR69IEQ4aHv" - }, - "execution_count": null, - "outputs": [] - }, - { - "cell_type": "markdown", - "source": [ - "Q2. Vous pouvez tester votre code sur les exemples suivants:\n", - "\n", - "\n", - "* $L('CCAG', 'CA') = 2$\n", - "* $L('CCGT', 'CGTCA') = 3$\n", - "* $L(AY678264^*, OQ870305^*) = 310$\n", - "\n", - "$^*$ ids genbank de deux sequences." - ], - "metadata": { - "id": "arFVwA6E5NWn" - } - }, - { - "cell_type": "markdown", - "source": [ - "# Exercice 2 : Algorithme de Smith-Waterman - version itérative" - ], - "metadata": { - "id": "erCpfG7O7BV-" - } - }, - { - "cell_type": "markdown", - "source": [ - "Q1. Ecrivez la fonction\n", - "\n", - "sw_fwd(x: str, y: str, cmap: dict, sigma: array, (go, ge): list) -> (array, array)\n", - "\n", - "qui construit les matrices $S$ et $B$ en utilisant l'algorithme de Smith-Waterman pour aligner les séquences x et y suivant le schéma d'évaluation donné par la matrice de substitution $\\Sigma$ et la fonction d'évaluation des trous $\\gamma(n)= g_o + g_e \\times n$. Le dictionnaire cmap donne la position des différents nucléotides dans la matrice $\\Sigma$. La fonction retourne la paire de matrices de score $S$ et de retour $B$." - ], - "metadata": { - "id": "rv2Y78y37IOd" - } - }, - { - "cell_type": "code", - "source": [ - "#Votre code ici" - ], - "metadata": { - "id": "njn3JB0b-WHj" - }, - "execution_count": null, - "outputs": [] - }, - { - "cell_type": "markdown", - "source": [ - "Q2. Ecrivez la fonction\n", - "\n", - "sw_bwd(x: str, y: str, S: array, B: array) -> (str, str, float)\n", - "\n", - "qui effectue l'etape de retour de l'algorithme de Smith-Waterman etant donné les séquences $x$ et $y$ et les matrices de score $S$ et de retour $B$. La fonction retourne un tuple contenant les alignements des séquences x et y et le score de l'alignement." - ], - "metadata": { - "id": "55n8mt9U-Wai" - } - }, - { - "cell_type": "code", - "source": [ - "#Votre code ici" - ], - "metadata": { - "id": "ij9JDpBm_UZ7" - }, - "execution_count": null, - "outputs": [] - }, - { - "cell_type": "markdown", - "source": [ - "Q3. Vous pouvez tester votre code en utilisant le schéma d'évaluation suivant :" - ], - "metadata": { - "id": "kwmxg2dxAiwS" - } - }, - { - "cell_type": "code", - "source": [ - "cmap = {\"A\": 0, \"T\": 1, \"G\": 2, \"C\": 3}\n", - "m = np.array([[1, -0.5, -0.5, -0.5],\n", - " [-0.5, 1, -0.5, -0.5],\n", - " [-0.5, -0.5, 1, -0.5],\n", - " [-0.5, -0.5, -0.5, 1]])\n", - "go = 0\n", - "ge = 0.5" - ], - "metadata": { - "id": "JUtYRFTBAwwZ" - }, - "execution_count": null, - "outputs": [] - }, - { - "cell_type": "markdown", - "source": [ - "* $SW('TCGC', 'CTTAG')$ retourne un score de $1.5$ à la position $(3,5)$ et l'alignement" - ], - "metadata": { - "id": "eMGh4K5aIFxE" - } - }, - { - "cell_type": "code", - "source": [ - "HTML(\"
x:TCG
y:TAG
\")" - ], - "metadata": { - "colab": { - "base_uri": "https://localhost:8080/", - "height": 60 - }, - "id": "joHNwJ9AIf6F", - "outputId": "a9206810-a083-4d86-8b14-38183f1dd80c" - }, - "execution_count": null, - "outputs": [ - { - "output_type": "execute_result", - "data": { - "text/plain": [ - "" - ], - "text/html": [ - "
x:TCG
y:TAG
" - ] - }, - "metadata": {}, - "execution_count": 18 - } - ] - }, - { - "cell_type": "markdown", - "source": [ - "* $SW(AY678264^*, OQ870305^*)$ retourne un score de $342.1$ à la position $(708,717)$ et l'alignement" - ], - "metadata": { - "id": "JJlU5yvZI43D" - } + { + "cell_type": "markdown", + "metadata": { + "id": "JJlU5yvZI43D" + }, + "source": [ + "* $SW(AY678264^*, OQ870305^*)$ retourne un score de $342.1$ à la position $(708,717)$ et l'alignement" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 80 }, + "id": "HUELvWKMFtIO", + "outputId": "976bab6f-f1fc-4c5a-c69c-8de02fc838d0" + }, + "outputs": [ { - "cell_type": "code", - "source": [ - "from IPython.display import HTML\n", - "HTML(\"
x:ATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGC-A-CATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAG---GGCGAGGGCGAGGGC--CGCC-CCTACGAGGGCACCCAGACCGC-CAAGCTGAAGGTG-ACCA-AGG---G-TGGCC---CCCT-GCCCTTCGCCT-GGGA-CATCCTGTCC--C--C-T-CAGTTCATGT-A-CGGCT-CCAAGGCCTACGTG-A--AGCAC--C--C--C--G-CCGACATCCCCG-A--CTAC-T--TGAAGCTG-TCCTTC--C--C-----CGA-GG--GCTTCAAGTGGGAGCG-CGTGATGAACTTCGAGGACGGCGGCGTGGTG-ACCG--T-GA-C-CCAGGAC-TC--CTCCCTGCAGGACGGCGAGTTCATCTACAAGGTG---AAGCTGCGCGGCACCAACTTCCCCT-CCGACGGCCCCGTA-ATGCA-GAAGAAGACCATGGGCTG--GGA-GGCCTCCTCCGAGCGGATGTACCCCGAGGA-CGGCGCC-CTGAAGGGCGAGATCAAGCAGA-GGCTGAAGC-TGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACA-AGGCCAAGAAG-CCCGTGCAGCTGCCCGGC-GCCTACAACGTCAACATCAAGT-TG----GA-CATCACCTCCCACAACGAGGA-CTAC-A-C-CA---T-C-G-TGGAACAGTACG-AACGCGCCGAGGGCCGCCACTCCAC-CGGCGGCATGGACGAGCTGTACAAG
y:ATGGTGAGCAAGGGCGAGGA-G----C-T-G--TTCA-C-CGG-GGTGGTGCCCATCCTGGT-CGAGC-TGGACGGCGACGTAAACGGCCACAAGTTC-AG--CGTGTCCGGCGAGGGCGAGGGCGATGCCACCTAC---GGCAAGCTGACC-CTGAAG-TTCATTTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCC-AC-CCTCGTGACCACCCTGACCTACGGCGTGCAGTGC-T-TCAGCCGCTACCCCGACC-ACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGC-GCACCATCTTCTTCAAGGACGACGGCAACTACAAGA-CCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGC-A--ACATC--C-TGGGGCACAAGCTG-G-AGTA-CAACTACAACAGCC-ACAACGTC-TATAT-CATG--GCCGA-CAA--GCAGAAGAACGG-CA--T-C-A-AGG-TGAACTTC-AAGATC--CGCCAC--AA---C---ATCGAG--GACGGC---AGCGTGCAGCTCGCCGACCACTACCA-GC--A-G--AACACC-CC--CATCGGCGACG--GCCCCGTGCTGCTGCCCGACAACC-ACTACCTGAGCACCCAGTCCGCCCTGAGCAA-A-GACCC-CAACGAGAAGC-GCGATCACATGGTCCTGCTGG---AGTTCGTGAC-CGCC----GCCGGGA-T-CACTC-TCGGCATGGACGAGCTGTACAAG
\")" + "data": { + "text/html": [ + "
x:ATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGC-A-CATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAG---GGCGAGGGCGAGGGC--CGCC-CCTACGAGGGCACCCAGACCGC-CAAGCTGAAGGTG-ACCA-AGG---G-TGGCC---CCCT-GCCCTTCGCCT-GGGA-CATCCTGTCC--C--C-T-CAGTTCATGT-A-CGGCT-CCAAGGCCTACGTG-A--AGCAC--C--C--C--G-CCGACATCCCCG-A--CTAC-T--TGAAGCTG-TCCTTC--C--C-----CGA-GG--GCTTCAAGTGGGAGCG-CGTGATGAACTTCGAGGACGGCGGCGTGGTG-ACCG--T-GA-C-CCAGGAC-TC--CTCCCTGCAGGACGGCGAGTTCATCTACAAGGTG---AAGCTGCGCGGCACCAACTTCCCCT-CCGACGGCCCCGTA-ATGCA-GAAGAAGACCATGGGCTG--GGA-GGCCTCCTCCGAGCGGATGTACCCCGAGGA-CGGCGCC-CTGAAGGGCGAGATCAAGCAGA-GGCTGAAGC-TGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACA-AGGCCAAGAAG-CCCGTGCAGCTGCCCGGC-GCCTACAACGTCAACATCAAGT-TG----GA-CATCACCTCCCACAACGAGGA-CTAC-A-C-CA---T-C-G-TGGAACAGTACG-AACGCGCCGAGGGCCGCCACTCCAC-CGGCGGCATGGACGAGCTGTACAAG
y:ATGGTGAGCAAGGGCGAGGA-G----C-T-G--TTCA-C-CGG-GGTGGTGCCCATCCTGGT-CGAGC-TGGACGGCGACGTAAACGGCCACAAGTTC-AG--CGTGTCCGGCGAGGGCGAGGGCGATGCCACCTAC---GGCAAGCTGACC-CTGAAG-TTCATTTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCC-AC-CCTCGTGACCACCCTGACCTACGGCGTGCAGTGC-T-TCAGCCGCTACCCCGACC-ACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGC-GCACCATCTTCTTCAAGGACGACGGCAACTACAAGA-CCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGC-A--ACATC--C-TGGGGCACAAGCTG-G-AGTA-CAACTACAACAGCC-ACAACGTC-TATAT-CATG--GCCGA-CAA--GCAGAAGAACGG-CA--T-C-A-AGG-TGAACTTC-AAGATC--CGCCAC--AA---C---ATCGAG--GACGGC---AGCGTGCAGCTCGCCGACCACTACCA-GC--A-G--AACACC-CC--CATCGGCGACG--GCCCCGTGCTGCTGCCCGACAACC-ACTACCTGAGCACCCAGTCCGCCCTGAGCAA-A-GACCC-CAACGAGAAGC-GCGATCACATGGTCCTGCTGG---AGTTCGTGAC-CGCC----GCCGGGA-T-CACTC-TCGGCATGGACGAGCTGTACAAG
" ], - "metadata": { - "colab": { - "base_uri": "https://localhost:8080/", - "height": 80 - }, - "id": "HUELvWKMFtIO", - "outputId": "976bab6f-f1fc-4c5a-c69c-8de02fc838d0" - }, - "execution_count": null, - "outputs": [ - { - "output_type": "execute_result", - "data": { - "text/plain": [ - "" - ], - "text/html": [ - "
x:ATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGC-A-CATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAG---GGCGAGGGCGAGGGC--CGCC-CCTACGAGGGCACCCAGACCGC-CAAGCTGAAGGTG-ACCA-AGG---G-TGGCC---CCCT-GCCCTTCGCCT-GGGA-CATCCTGTCC--C--C-T-CAGTTCATGT-A-CGGCT-CCAAGGCCTACGTG-A--AGCAC--C--C--C--G-CCGACATCCCCG-A--CTAC-T--TGAAGCTG-TCCTTC--C--C-----CGA-GG--GCTTCAAGTGGGAGCG-CGTGATGAACTTCGAGGACGGCGGCGTGGTG-ACCG--T-GA-C-CCAGGAC-TC--CTCCCTGCAGGACGGCGAGTTCATCTACAAGGTG---AAGCTGCGCGGCACCAACTTCCCCT-CCGACGGCCCCGTA-ATGCA-GAAGAAGACCATGGGCTG--GGA-GGCCTCCTCCGAGCGGATGTACCCCGAGGA-CGGCGCC-CTGAAGGGCGAGATCAAGCAGA-GGCTGAAGC-TGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACA-AGGCCAAGAAG-CCCGTGCAGCTGCCCGGC-GCCTACAACGTCAACATCAAGT-TG----GA-CATCACCTCCCACAACGAGGA-CTAC-A-C-CA---T-C-G-TGGAACAGTACG-AACGCGCCGAGGGCCGCCACTCCAC-CGGCGGCATGGACGAGCTGTACAAG
y:ATGGTGAGCAAGGGCGAGGA-G----C-T-G--TTCA-C-CGG-GGTGGTGCCCATCCTGGT-CGAGC-TGGACGGCGACGTAAACGGCCACAAGTTC-AG--CGTGTCCGGCGAGGGCGAGGGCGATGCCACCTAC---GGCAAGCTGACC-CTGAAG-TTCATTTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCC-AC-CCTCGTGACCACCCTGACCTACGGCGTGCAGTGC-T-TCAGCCGCTACCCCGACC-ACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGC-GCACCATCTTCTTCAAGGACGACGGCAACTACAAGA-CCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGC-A--ACATC--C-TGGGGCACAAGCTG-G-AGTA-CAACTACAACAGCC-ACAACGTC-TATAT-CATG--GCCGA-CAA--GCAGAAGAACGG-CA--T-C-A-AGG-TGAACTTC-AAGATC--CGCCAC--AA---C---ATCGAG--GACGGC---AGCGTGCAGCTCGCCGACCACTACCA-GC--A-G--AACACC-CC--CATCGGCGACG--GCCCCGTGCTGCTGCCCGACAACC-ACTACCTGAGCACCCAGTCCGCCCTGAGCAA-A-GACCC-CAACGAGAAGC-GCGATCACATGGTCCTGCTGG---AGTTCGTGAC-CGCC----GCCGGGA-T-CACTC-TCGGCATGGACGAGCTGTACAAG
" - ] - }, - "metadata": {}, - "execution_count": 15 - } + "text/plain": [ + "" ] - }, - { - "cell_type": "markdown", - "source": [ - "# Exercice 3 : Distribution des scores d’alignement pour des séquences aléatoires\n", - "\n", - "Pour tester si un alignement reflète une réelle similarité biologique, on va évaluer la distribution des scores d’alignement pour des paires de séquences aléatoires." - ], - "metadata": { - "id": "Q5jVeLfgMMtA" - } - }, - { - "cell_type": "markdown", - "source": [ - "Q1. En considérant deux séquences aléatoires de même taille N, où chaque nucléotide apparaît avec une probabilité uniforme de ¼, calculer le score moyen attendu pour une superposition sans trou dans le cas où une identité vaut +1 et une différence vaut 0." - ], - "metadata": { - "id": "6xyXw0HsMQGf" - } - }, - { - "cell_type": "markdown", - "source": [ - "```markdown\n", - "Votre réponse ici\n", - "```" - ], - "metadata": { - "id": "meF18gt-Mhcn" - } - }, - { - "cell_type": "markdown", - "source": [ - "Q2. La question précédente peut se resoudre analytiquement car on ne considère pas de trou. Pour étendre le résultat precedent à un alignement avec trous, on va se baser sur la simulation de séquences aleatoires.\n", - "\n", - "Générez $R$ paires de séquences aléatoires de tailles $N$ avec des probabilitées uniformes d'apparition de nucléotides $p_A = p_T = p_G = p_C = $ ¼. Affichez sous forme de violinplots les distribution des scores d'alignements entre chaque paire, obtenu par :\n", - " 1. un alignement sans trou (cf. Q1) ;\n", - " 2. un alignement local via Smith-Waterman (utilisez le code de l'exercice précédent)\n", - "\n", - "Utilisez le schéma d'évaluation suivant :" - ], - "metadata": { - "id": "fP5_mHnYMkNI" - } - }, - { - "cell_type": "code", - "source": [ - "rmap = {\"A\": 0, \"T\": 1, \"G\": 2, \"C\": 3}\n", - "sigma = np.array([[1, -0.5, -0.5, -0.5],\n", - " [-0.5, 1, -0.5, -0.5],\n", - " [-0.5, -0.5, 1, -0.5],\n", - " [-0.5, -0.5, -0.5, 1]])\n", - "go =0\n", - "ge = 0.5" - ], - "metadata": { - "id": "akUVqotnOLkH" - }, - "execution_count": null, - "outputs": [] - }, - { - "cell_type": "code", - "source": [ - "#Votre code ici" - ], - "metadata": { - "id": "UX0afNaqOVZ2" - }, - "execution_count": null, - "outputs": [] - }, - { - "cell_type": "markdown", - "source": [ - "Q3. Qu'observez-vous ?" - ], - "metadata": { - "id": "UNn9fUuXO4Le" - } - }, - { - "cell_type": "markdown", - "source": [ - "```markdown\n", - "Votre réponse ici\n", - "```" - ], - "metadata": { - "id": "dSQEl0XXO8IG" - } - }, - { - "cell_type": "markdown", - "source": [ - "Q4. Quelle conclusion peut-on en tirer sur la significativité d'un alignement ?" - ], - "metadata": { - "id": "xHfVXpQhf15n" - } - }, - { - "cell_type": "markdown", - "source": [ - "```markdown\n", - "Votre réponse ici\n", - "```" - ], - "metadata": { - "id": "5KjhEeHDgDns" - } + }, + "execution_count": 54, + "metadata": {}, + "output_type": "execute_result" } - ] -} \ No newline at end of file + ], + "source": [ + "from IPython.display import HTML\n", + "HTML(\"
x:ATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGC-A-CATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAG---GGCGAGGGCGAGGGC--CGCC-CCTACGAGGGCACCCAGACCGC-CAAGCTGAAGGTG-ACCA-AGG---G-TGGCC---CCCT-GCCCTTCGCCT-GGGA-CATCCTGTCC--C--C-T-CAGTTCATGT-A-CGGCT-CCAAGGCCTACGTG-A--AGCAC--C--C--C--G-CCGACATCCCCG-A--CTAC-T--TGAAGCTG-TCCTTC--C--C-----CGA-GG--GCTTCAAGTGGGAGCG-CGTGATGAACTTCGAGGACGGCGGCGTGGTG-ACCG--T-GA-C-CCAGGAC-TC--CTCCCTGCAGGACGGCGAGTTCATCTACAAGGTG---AAGCTGCGCGGCACCAACTTCCCCT-CCGACGGCCCCGTA-ATGCA-GAAGAAGACCATGGGCTG--GGA-GGCCTCCTCCGAGCGGATGTACCCCGAGGA-CGGCGCC-CTGAAGGGCGAGATCAAGCAGA-GGCTGAAGC-TGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACA-AGGCCAAGAAG-CCCGTGCAGCTGCCCGGC-GCCTACAACGTCAACATCAAGT-TG----GA-CATCACCTCCCACAACGAGGA-CTAC-A-C-CA---T-C-G-TGGAACAGTACG-AACGCGCCGAGGGCCGCCACTCCAC-CGGCGGCATGGACGAGCTGTACAAG
y:ATGGTGAGCAAGGGCGAGGA-G----C-T-G--TTCA-C-CGG-GGTGGTGCCCATCCTGGT-CGAGC-TGGACGGCGACGTAAACGGCCACAAGTTC-AG--CGTGTCCGGCGAGGGCGAGGGCGATGCCACCTAC---GGCAAGCTGACC-CTGAAG-TTCATTTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCC-AC-CCTCGTGACCACCCTGACCTACGGCGTGCAGTGC-T-TCAGCCGCTACCCCGACC-ACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGC-GCACCATCTTCTTCAAGGACGACGGCAACTACAAGA-CCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGC-A--ACATC--C-TGGGGCACAAGCTG-G-AGTA-CAACTACAACAGCC-ACAACGTC-TATAT-CATG--GCCGA-CAA--GCAGAAGAACGG-CA--T-C-A-AGG-TGAACTTC-AAGATC--CGCCAC--AA---C---ATCGAG--GACGGC---AGCGTGCAGCTCGCCGACCACTACCA-GC--A-G--AACACC-CC--CATCGGCGACG--GCCCCGTGCTGCTGCCCGACAACC-ACTACCTGAGCACCCAGTCCGCCCTGAGCAA-A-GACCC-CAACGAGAAGC-GCGATCACATGGTCCTGCTGG---AGTTCGTGAC-CGCC----GCCGGGA-T-CACTC-TCGGCATGGACGAGCTGTACAAG
\")" + ] + }, + { + "cell_type": "code", + "execution_count": 55, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "('TGGTGAGCA__AG_GGCG_AG_G_AGGA_TAACATG_G__CCA_TCATCA_AGGAGTTCATGCGC__TTCAAGGTGCACA_TGGA_GG_GCTCCGTGAACGGCCAC_GA_GTTCGAGATCGAG_GGCGAGGGCG_AGG_GCCGC_CCCTACGAGGGCACCCAGACCGC_CAAGCTGAAGGTGAC_CAAGGGTGGCCCCCTGCC_CTTCGCCTGG__GACATCCTGTCCCCTCA_GTTCATGTACGG_CTCCAAGGCCTACGTGAAG_CACCCCG__C___CGACATC__CCCGACTACTT_GA_AGCTGTCCTTCCCCGAGGGCTTCAAGTG__GGAGCGCG_TGATGAACTTC___GAGGAC_GG_____C__G__GCGTGGTG_A__C_CG__TGACCCAGGAC_TCCTC_CCTGCAGGA_CG_GC____GAG_TTC_ATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGC__CTCCTC_CGAGCGGATGTACCCCGA_GGACGGC__GCCCTGAAGGGCGAG_ATC_AAG_C_A____GAG_GCTG__A_AGC_T_GAAGGACGGCGGC___C_ACTACGAC_G__C_TGAGGTCAAGACCA_CCTACAA__GGCCAAGAAGCCC_GTGCAGCTGCCCGGC_GCC__TACAAC_GTCAACATCAAGT_TGGAC_ATC___ACCTCCC_AC__AACGAG_GACTACA____CCATCGTGGAACAGTACG_AAC_GC_GCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAGTAA', 'TGG_G_GCATTCGCTACGAAGAGAATGAGTAA_AGGAGAAGAACTTTTCACTGGAGTT_GT_CCCAATTCTTGTTG_A_ATTAGATGGTGAT__GTTAATGGGCACAAATTTTC_TG_TC_AGTGGAGAGGGTGAAGGTGATGCAACATAC___GGAAAACTTACC_CTTAA_ATTTATTTG_CACTA__CTGGAAAACTACCTGTTC_CATGGCCAACA_CTTGT_CACT_ACTTTCACCTATGGTGTTCAATG_CT_TTTCAAGATACCCAGATCATATGA_AGCGGCACGACTTCTTCAAGAGC_G_CCATGCCTGAGGG_AT_ACGTGCAGGAGAG_GACCATCTTCTTCAAAGACGACGGGAACTACAAGACACGTGCTGAAGTCAAGTTTGAGGGA_GACACCCTCGTCAACAGGATCGAGCTTAAGGGAATCGAT_TTCAA_G_G_AG__G_ACGG_A__AACAT__CCT____CGGCCAC__AA_GTTG__GAATA_CA___ACT___A__CAACTCC_CAC_AAC_G_TATACATC_ATGGCCGACAAG__CAAAAGAACG_GCATCAAAGCCAACTTCAAGACCCGCCACAACATCGAA_GACGGCGGCGTGCAACT_CG_CTGATCATTA__TCAACAAAATACTCCAATTGGCGATG__GCCCTGTCCTTTTACCAGACAACCATTAC__CTGTCCACA_CAA_TCTGCCCTTTCGAAAGATCCCAACGAAAAGAGAGACCACATGGTCCTTC_TTG___AGTTTGTAACAGCTG_C__TGG__G__ATTACA_C_ATGGCATGGATGAACTATACAAATAA', 277.5)\n" + ] + } + ], + "source": [ + "genbank1 = (\"atggtgagcaagggcgaggaggataacatggccatcatcaaggagttcatgcgcttcaaggtgcacatggagggctccgtgaacggccacgagttcgagatcgagggcgagggcgagggccgcccctacgagggcacccagaccgccaagctgaaggtgaccaagggtggccccctgcccttcgcctgggacatcctgtcccctcagttcatgtacggctccaaggcctacgtgaagcaccccgccgacatccccgactacttgaagctgtccttccccgagggcttcaagtgggagcgcgtgatgaacttcgaggacggcggcgtggtgaccgtgacccaggactcctccctgcaggacggcgagttcatctacaaggtgaagctgcgcggcaccaacttcccctccgacggccccgtaatgcagaagaagaccatgggctgggaggcctcctccgagcggatgtaccccgaggacggcgccctgaagggcgagatcaagcagaggctgaagctgaaggacggcggccactacgacgctgaggtcaagaccacctacaaggccaagaagcccgtgcagctgcccggcgcctacaacgtcaacatcaagttggacatcacctcccacaacgaggactacaccatcgtggaacagtacgaacgcgccgagggccgccactccaccggcggcatggacgagctgtacaagtaa\").upper()\n", + "genbank2 = (\"atggtctccttcaaatctctcctagttctctgttgcgctgcccttggggcattcgctacgaagagaatgagtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcacctatggtgttcaatgcttttcaagatacccagatcatatgaagcggcacgacttcttcaagagcgccatgcctgagggatacgtgcaggagaggaccatcttcttcaaagacgacgggaactacaagacacgtgctgaagtcaagtttgagggagacaccctcgtcaacaggatcgagcttaagggaatcgatttcaaggaggacggaaacatcctcggccacaagttggaatacaactacaactcccacaacgtatacatcatggccgacaagcaaaagaacggcatcaaagccaacttcaagacccgccacaacatcgaagacggcggcgtgcaactcgctgatcattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataa\").upper()\n", + "\n", + "S,B = sw_fwd(genbank1, genbank2, cmap, m, go, ge)\n", + "\n", + "print(sw_bwd(genbank1, genbank2, S, B))" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "Q5jVeLfgMMtA" + }, + "source": [ + "# Exercice 3 : Distribution des scores d’alignement pour des séquences aléatoires\n", + "\n", + "Pour tester si un alignement reflète une réelle similarité biologique, on va évaluer la distribution des scores d’alignement pour des paires de séquences aléatoires." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "6xyXw0HsMQGf" + }, + "source": [ + "Q1. En considérant deux séquences aléatoires de même taille N, où chaque nucléotide apparaît avec une probabilité uniforme de ¼, calculer le score moyen attendu pour une superposition sans trou dans le cas où une identité vaut +1 et une différence vaut 0." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "meF18gt-Mhcn" + }, + "source": [ + "```markdown\n", + "Votre réponse ici\n", + "```" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "fP5_mHnYMkNI" + }, + "source": [ + "Q2. La question précédente peut se resoudre analytiquement car on ne considère pas de trou. Pour étendre le résultat precedent à un alignement avec trous, on va se baser sur la simulation de séquences aleatoires.\n", + "\n", + "Générez $R$ paires de séquences aléatoires de tailles $N$ avec des probabilitées uniformes d'apparition de nucléotides $p_A = p_T = p_G = p_C = $ ¼. Affichez sous forme de violinplots les distribution des scores d'alignements entre chaque paire, obtenu par :\n", + " 1. un alignement sans trou (cf. Q1) ;\n", + " 2. un alignement local via Smith-Waterman (utilisez le code de l'exercice précédent)\n", + "\n", + "Utilisez le schéma d'évaluation suivant :" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "id": "akUVqotnOLkH" + }, + "outputs": [], + "source": [ + "rmap = {\"A\": 0, \"T\": 1, \"G\": 2, \"C\": 3}\n", + "sigma = np.array([[1, -0.5, -0.5, -0.5],\n", + " [-0.5, 1, -0.5, -0.5],\n", + " [-0.5, -0.5, 1, -0.5],\n", + " [-0.5, -0.5, -0.5, 1]])\n", + "go =0\n", + "ge = 0.5" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "id": "UX0afNaqOVZ2" + }, + "outputs": [], + "source": [ + "#Votre code ici" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "UNn9fUuXO4Le" + }, + "source": [ + "Q3. Qu'observez-vous ?" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "dSQEl0XXO8IG" + }, + "source": [ + "```markdown\n", + "Votre réponse ici\n", + "```" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "xHfVXpQhf15n" + }, + "source": [ + "Q4. Quelle conclusion peut-on en tirer sur la significativité d'un alignement ?" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "5KjhEeHDgDns" + }, + "source": [ + "```markdown\n", + "Votre réponse ici\n", + "```" + ] + } + ], + "metadata": { + "colab": { + "authorship_tag": "ABX9TyNSXnqaXAUgZK9rmJ1TWbGo", + "provenance": [] + }, + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, + "nbformat": 4, + "nbformat_minor": 1 +}