Python for Bioinformatics for Beginners | Calculate GC Content in Multiple Fasta Files

Опубликовано: 13 Май 2021
на канале: Bioinformatics Coach

1,568

This tutorial shows you how to read a fasta file and calculate the GC content of sequences using the python bioinformatics package, biopython.

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Materials
________________________________________________________________________________________________

Read fasta files
   • Python for Bioinformatics for Beginners | ...

Download codes and notebook here
https://github.com/vappiah/Python-Bio...

How to install python libraries
   • Install python packages using pip

Download fasta sequence files here
https://www.ncbi.nlm.nih.gov/nuccore/... V521 Strain
https://www.ncbi.nlm.nih.gov/nuccore/... M48 Strain
https://www.ncbi.nlm.nih.gov/nuccore/... P10 Strain
https://www.ncbi.nlm.nih.gov/nuccore/... AR465
https://www.ncbi.nlm.nih.gov/nuccore/... R50

Chapters
________________________________________________________________________________________________
00:00:10:15 Outline of the tutorial
01:17 Download Fasta Files
02:59 Import Python libraries
03:37 Set directory containing files
04:02 Get all filenames using glob module
06:07 Create a function for the sequence analysis
09:43 Use iterations to automate the the analysis
10:46 Analyze sequences and save result to pandas dataframe
15:18 Create Dataframe using pandas
17:13 Save dataframe to output file

Commands used

from Bio import SeqIO
SeqIO.parse
Bio.SeqUtils
GC

#Bioinformatics #DataScience #python

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