BioPython – qblast() timeout every time, running from python shell
I am a new user to BioPython. I have set up my virtual env and installed BioPython via pip inside the venv.
Finding similar DNA sequence in a specific organism with Biopython’s Blast module
I am trying to find a DNA sequence homologous to a given coding sequence in a specific organism (E. fergusoni, to root an E. coli genes phylogeny)
I want to blast one of my focal species’ sequence and get back all sequence from E. fergusoni that have between 80% and 98% similarity on the whole segment.
This work prety well on the NCBI online version of blast, by setting “Escherichia fergusonii (taxid:564)” in the “Organism” field. However, I want to automatise this process to be able to run it quickly on a large set of disinct E. coli genes.