November 2024
Intermediate to advanced
456 pages
11h 58m
French
Content preview from Maîtriser Python pour la bioinformatique
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Chapitre 9. Graphes de chevauchement : Assemblage de séquences à l'aide de K-mères partagées
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Un graphe est une structure utilisée pour représenter des relations par paires entre des objets. Comme décrit dans le défi Rosalind GRPH, le but de cet exercice est de trouver des paires de séquences qui peuvent être jointes en utilisant un chevauchement de la fin d'une séquence au début d'une autre. L'application pratique de ceci serait de joindre de courtes lectures d'ADN dans des séquences contiguës plus longues(contigs) ou même des génomes entiers. Pour commencer, je ne m'intéresserai qu'à l'assemblage de deux séquences, mais une deuxième version du programme utilisera une structure de graphe qui peut assembler n'importe quel nombre de séquences pour obtenir un assemblage complet. Dans cette implémentation, les régions de chevauchement utilisées pour assembler les séquences doivent être des correspondances exactes. Les assembleurs du monde réel doivent permettre une variation de la taille et de la composition des séquences qui se chevauchent.
Tu apprendras :
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Comment utiliser les k-mères pour créer des graphes de chevauchement.
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Comment enregistrer les messages d'exécution dans un fichier
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Comment l'utiliser
collections.defaultdict() -
Comment utiliser l'intersection d'ensembles pour trouver des éléments communs entre des collections.
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Comment utiliser ...
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I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.