We will now do some basic analysis on DNA sequences. We will work with FASTA files and do some manipulation, such as reverse complementing or transcription. As with the previous recipe, we will use Biopython, which you installed in Chapter 1, Python and the Surrounding Software Ecology. These two recipes provide you with the necessary introductory building blocks in which we will perform all the modern next-generation sequencing analysis, and then genome processing in this and the next chapter.
If you are using notebooks, then open 01_NGS/Basic_Sequence_Processing.ipynb. If not, you will need to download a FASTA sequence. We will use the human lactase gene as an example; you can get this using the knowledge you got from the previous recipe using Entrez research interface:
from Bio import Entrez, SeqIO Entrez.email = "[email protected]" hdl = Entrez.efetch(db='nucleotide', id=['NM_002299'], rettype='fasta') # Lactase gene seq = SeqIO.read(hdl,...