Multiple Sequence Alignment (MSA) in R (Bioinformatics S11E2) скачать в хорошем качестве

Multiple Sequence Alignment (MSA) in R (Bioinformatics S11E2)

How to use the msa and seqinr R libraries to compute and visualize Pairwise and Multiple Sequence Alignments in the R programming language. R code at 29:06. This lecture is a deep dive into everything related to multiple sequence alignment: Tools, Pitfalls, Transcription Factor Binding Sites (TFBS), and Positional Weight Matrices (PWM). Lectures @ https://dannyarends.nl/bioinformatik/ Programming Assignments and Answers @ https://dannyarends.nl/bioinfo/ Playlist:    • Bioinformatics for Plant and Animal sciences   Chapters: 00:00 Welcome back 00:16 ClustalW 3-step alignment overview 03:30 ClustalW consensus sequence symbols 04:56 Multiple alignment pitfalls and example 06:49 Different multiple sequence alignment (MSA) tools 08:14 Future goal: Pairwise and Multiple 3D Structural Alignment 11:00 Motifs as consensus sequence and searching in DNA 12:50 String Motifs 14:27 Positional weight matrices (PWM) Motifs 15:44 Creating a Positional weight matrices (PWM) 18:45 Future goal: Nucleotide Dependent (ND) weight matrices 20:17 Transcription Factor Binding Site (TFBS) Motif databases 21:51 Finding Motifs through phylogeny analysis 22:56 Tools overview 25:36 Multiple Sequence Alignment in denovo genome assembly 29:06 Multiple Sequence Alignment in R (install & load) 30:01 AAStringSet (or DNAStringSet) in R 31:27 ClustalW and Muscle alignment in R 32:56 The seqinr library in R to compute similarity and distances 36:07 Multiple Sequence Alignment phylogeny plot in R 40:15 Overview and end of stream This is a live-stream recording of the MSc and PhD lecture series: Bioinformatics for plant and animal sciences, given digitally during the Covid19 pandemic at the Humboldt University in Berlin organized and lectured by Dr Danny Arends. Thanks for taking an interest in my channel 😄If you've made it this far down, support me by giving a like or subscribing. Join me during my live streams Thursday afternoons on Twitch @   / dannyarends   This work is licensed under version 3.0 of the Creative Commons CC-BY license. For more information see http://creativecommons.org/licenses/b... #bioinformatics #computationalbiology #lectureseries #programmingforstudents #playlist #molecularbiology #science #englishstream #msc #phd #assignments #answers #academicyoutube #academia #msa #seqinr #pwm #denovo #clustalw #aastringset #dnastringset #nucleotide #ND #transcription #transcriptionfactor #TFBS #motifs #phylogeny #consensus